Search Results (82)

Tree diseases affecting Camellia japonica have emerged as a significant threat to the health and longevity of this ornamental tree, particularly in countries where this tree species is widely distributed and cultivated. Among these, Pestalotiopsis spp. have been frequently reported and are considered one of the most impactful fungal pathogens, causing leaf blight or leaf spot, in multiple countries. Understanding the etiology and distribution of these diseases is essential for effective management and conservation of C. japonica populations. The traditional methods based on pathogen isolation and pure culture cultivation for diagnosis of tree diseases are labor intensive and time-consuming. In addition, the frequent coexistence of the major pathogens with other endophytes within a single C. japonica tree, coupled with inconsistent symptom expression and the occurrence of pathogens in asymptomatic hosts, further complicates disease diagnosis. These challenges highlight the urgent need to develop more rapid, accurate, and efficient diagnostic or monitoring tools to improve disease monitoring and management on trees, including C. japonica. To address these challenges, we applied a metagenomic approach to screen fungal communities within C. japonica trees. This method enabled comprehensive detection and characterization of fungal taxa present in symptomatic and asymptomatic tissues. By analyzing the correlation between fungal dominance and symptom expression, we identified key pathogenic taxa associated with disease manifestation. To validate the metagenomic approach, we employed a combined strategy integrating metagenomic screening and traditional fungal isolation to monitor foliar diseases in C. japonica. The correlation between dominant taxa and symptom expression was confirmed. Simultaneously, traditional isolation enabled the identification of a novel species, Pestalotiopsis, as the causal agent of leaf spot disease on C. japonica. In addition to confirming previously known pathogens, our study led to the discovery and preliminary characterization of a novel fungal taxon with pathogenic potential. Our findings provide critical insights into the fungal community of C. japonica and lay the groundwork for developing improved, rapid diagnostic tools for effective disease monitoring and management of tree diseases. Full article

Long-term monoculture of poplar plantations for industrial material production has been widely reported to cause severe soil degradation, while the presence of understory vegetation might enhance soil nitrogen (N) transformation and supply. This study employed a field experiment using a randomized block design with three blocks and four understory treatments, including understory removal, N-fixing species planting, single-species retention, and diverse vegetation retention, in poplar plantations on a mid-latitude alluvial plain in China over 6 years to assess the effects of different species and richness of understory on soil N transformation and related microbial traits via ¹⁵N assays and shotgun metagenomics. The results showed that understory removal significantly reduced soil N transformation rates, bacterial abundance, and gene abundance associated with N transformation. Compared to a single-species understory, retaining a diverse understory with high species richness significantly increased soil gross N transformation rate of mineralization by 149%, nitrification by 221%, and immobilization by 85%; comprehensively enriched dominant bacterial phyla; and elevated gene abundances of gdh_K15371, ureB, hao, and amoA_B associated with N transformation. No significant difference in N transformation rates existed between N-fixing species planting treatment and single-species retention treatment, while N-fixing species planting treatment specifically promoted the soil bacterial phyla Nitrospirae and Chloroflexi, and increased the gene abundances of gdh_K15371 and hao. These findings demonstrate that both introducing N-fixing species and an increase in species richness of the understory effectively promoted soil N transformation but that different underlying mechanisms existed. Planting N-fixing species selectively increased the soil bacterial phyla of Nitrospirae and Chloroflexi, whereas the increase in species richness broadly enriched soil bacterial diversity, thereby inducing the enrichment of the functional genes and enhancing soil N transformation. In conclusion, both planting N-fixing species and retaining diverse understory vegetation were effective strategies for maintaining sustainable management of poplar plantations by increasing soil N availability. Full article

Bobcats (Lynx rufus) are an iconic North American predator; however, there is limited knowledge regarding their associated parasites. In this case study, we used a metagenomic approach to identify associated viruses and helminth species from a deceased bobcat. We determined the full mitochondrial genome of the bobcat and three helminths, i.e., tapeworm (Taenia sp.), stomach worm (Physaloptera sp.), and lung worm (Metathelazia sp.). Furthermore, we identified four circovirids; two (identified in a tapeworm and fecal swab) are members of the genus Circovirus and share 96.7% genome-wide identity between isolates and 87.4–88.6% identity with members of the species Circovirus miztontli. These appear to infect vertebrate species common to the Sonoran Desert, which could be a rodent preyed upon by the bobcat, and/or bobcat itself. The other two circovirids are novel members of the genus Cyclovirus (both identified in a tapeworm), one sharing 99.8% with those in the species Cyclovirus misi from a rodent and the other <67.3% with all other Cycloviruses. Our data support that these two Cycloviruses are likely tapeworm-infecting; however, more studies are needed to confirm the host. These findings enhance our understanding of viruses and helminths in bobcats, emphasizing the need for further research to unravel the ecology of parasites in these elusive predators. Full article

Rice is a major crop for half of the world’s population, and nitrogen (N) fertilizers play a crucial role in its production. However, imbalanced N fertilizer uses and traditional fertilization practices have led to low nitrogen use efficiency (NUE), increased N footprints, and reduced rice yields and farmers’ income. There are limited studies where the integration of both agronomic and molecular advancements to enhance NUE is discussed, particularly in developing countries. This review highlights novel agronomic and molecular strategies to enhance NUE, rice yields, and profitability, while minimizing environmental impact. The agronomic strategies include the 4R Nutrient Stewardship framework, enhanced efficiency nitrogen fertilizers (EENFs), nano-fertilizers, biochar-based fertilizers, biological N fixation, and sensor-based fertilizer management in major rice-growing countries. The molecular mechanisms focus on N uptake, assimilation, and utilization, highlighting the role of hormones, key genes, transcription factors (TFs), and regulatory pathways. Moreover, we examine promising rice genotypes and cultivars with improved NUE and grain yield. Additionally, this paper offers deep insights into recent advancements in molecular genetics, such as multi-omics approaches (transcriptomics, metabolomics, and metagenomics), the Genome-Wide Association Study (GWAS), Quantitative Traits Loci mapping (QTLs), Single Nucleotide Polymorphisms (SNPs) analysis, and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR-Cas9)-mediated genome editing, which serve as valuable tools for developing rice cultivars with enhanced NUE and grain yield. Full article

Plant-phyllosphere feedback (PPF) is an ecological process in which phyllosphere microbiota, originating from plant litter, are transmitted via aerosols and subsequently influence the growth of conspecific or heterospecific plants. However, the cross-species generality of this mechanism and its role in invasive plant success remain to be fully elucidated. This study systematically examined PPF effects using three invasive/native congeneric plant pairs from distinct families (Phytolaccaceae, Asteraceae, and Amaranthaceae) in Jiangxi Province, China. Key findings include the following: (1) Wide conspecific negative feedback across families, with four of six species exhibiting 6.2–12.7% biomass reduction under their own litter treatments (p < 0.05). (2) Comparable feedback intensity between invasive and native species, as indicated by average pairwise indices (invasive I = −0.05 vs. native I = −0.04; p = 0.15). Notably, the invasive species Phytolacca americana uniquely showed a positive biomass response (+7.1%), though underlying mechanisms (phytochemical or microbial) were not investigated. (3) Lack of correlation between PPF strength and plant functional traits or phylogenetic distance, as indicated by Mantel tests (p > 0.8), in contrast to the trait/phylogeny associations commonly observed in soil feedback systems. This study provided the first evidence of PPF universality across multiple plant families—previously documented only within Asteraceae—and highlights the potential microbial-mediated advantages in plant invasions. Future research should integrate spatiotemporal metagenomic and metabolomic approaches to decipher the dynamic pathogen/microbe networks and their phytochemical interactions. Full article

Air pollution has been widely recognized as a risk factor for neurological disorders, and the gut microbiome may play a mediating role. However, current evidence remains limited. In this study, a mouse model was employed with continuous exposure to real-time air pollution from conception to late adolescence. Effects of growth-stage air pollution exposure on the gut microbiome, host metabolites, and brain tissue were assessed. Pathological damage in the hippocampus and cortex was observed. Fecal metagenomic sequencing revealed alterations in both compositions and functions of the gut microbiome. Metabolic disturbances in unsaturated fatty acids and glycerophospholipids were identified in the intestine, serum, and brain tissues, with significant changes in metabolites (e.g., gamma-linolenic acid, alpha-linolenic acid, docosahexaenoic acid (DHA), phosphatidylethanolamine (PE), phosphatidylcholine (PC) and phosphatidylserine (PS). Serum levels of the pro-inflammatory mediator leukotriene C4 were also elevated. Correlation analysis identified a group of different gut microbiome species that were associated with host metabolites. Furthermore, mediation analysis showed that intestinal and serum metabolites mediated the associations between the key gut microbiome and brain microbiome. These findings indicate that the metabolic crosstalk in the gut–brain axis mediates the neuronal damage in mice induced by growth-stage air pollution exposure, potentially through pathways involving lipid metabolism and inflammation. Full article

Microbial symbioses deal with the symbiotic interactions between a given microorganism and another host. The most widely known and investigated microbial symbiosis is the association between leguminous plants and nitrogen-fixing rhizobia. It is one of the best-studied plant–microbe interactions that occur in the soil rhizosphere and one of the oldest plant–microbe interactions extensively studied for the past several decades globally. Until recently, it used to be a common understanding among scientists in the field of rhizobia and microbial ecology that the root nodules of thousands of leguminous species only contain nitrogen-fixing symbiotic rhizobia. With the advancement of molecular microbiology and the coming into being of state-of-the-art biotechnology innovations, including next-generation sequencing, it has now been revealed that rhizobia living in the root nodules of legumes are not alone. Microbiome studies such as metagenomics of the root nodule microbial community showed that, in addition to symbiotic rhizobia, other bacteria referred to as non-rhizobial endophytes (NREs) exist in the nodules. This review provides an insight into the occurrence of non-rhizobial endophytes in the root nodules of several legume species and the beneficial roles of the tripartite interactions between the legumes, the rhizobia and the non-rhizobial endophytes (NREs). Full article

Soybean is a vital crop globally and a key source of food, feed, and biofuel. With advancements in high-throughput technologies, soybeans have become a key target for genetic improvement. This comprehensive review explores advances in multi-omics, artificial intelligence, and economic sustainability to enhance soybean resilience and productivity. Genomics revolution, including marker-assisted selection (MAS), genomic selection (GS), genome-wide association studies (GWAS), QTL mapping, GBS, and CRISPR-Cas9, metagenomics, and metabolomics have boosted the growth and development by creating stress-resilient soybean varieties. The artificial intelligence (AI) and machine learning approaches are improving genetic trait discovery associated with nutritional quality, stresses, and adaptation of soybeans. Additionally, AI-driven technologies like IoT-based disease detection and deep learning are revolutionizing soybean monitoring, early disease identification, yield prediction, disease prevention, and precision farming. Additionally, the economic viability and environmental sustainability of soybean-derived biofuels are critically evaluated, focusing on trade-offs and policy implications. Finally, the potential impact of climate change on soybean growth and productivity is explored through predictive modeling and adaptive strategies. Thus, this study highlights the transformative potential of multidisciplinary approaches in advancing soybean resilience and global utility. Full article

Climate change heightens the threat of infectious diseases in Europe, necessitating innovative surveillance methods. Based on 390 scientific papers, for the first time, this review associates climate-related pathogens, data related to their presence in wastewater, and associated available genomic detection methods. This deep analysis reveals a wide range of pathogens that can be tracked through methods such as quantitative and digital PCR, as well as genomic pathogen enrichment in combination with sequencing and metagenomics. Nevertheless, significant gaps remain in the development of methods, particularly for vector-borne pathogens, and in their general harmonization relating to performance criteria. By offering an overview of recent advancements while identifying critical gaps, we advocate for collaborative research and validation to integrate detection techniques into surveillance frameworks. This will enhance public health resilience against emerging infectious diseases driven by climate change. Full article

Introduction: Nosocomial lower respiratory tract infections (nLRTIs), including hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), remain significant challenges due to high mortality, morbidity, and healthcare costs. Implementing accurate and timely diagnostic strategies is pivotal for guiding optimized antimicrobial therapy and addressing the growing threat of antimicrobial resistance. Areas Covered: This review examines emerging microbiological diagnostic methods for nLRTIs. Although widely utilized, traditional culture-based techniques are hindered by prolonged processing times, limiting their clinical utility in timely decision-making. Advanced molecular tools, such as real-time PCR and multiplex PCR, allow rapid pathogen identification but are constrained by predefined panels. Metagenomic next-generation sequencing (mNGS) provides comprehensive pathogen detection and resistance profiling yet faces cost, complexity, and interpretation challenges. Non-invasive methods, including exhaled breath analysis using electronic nose (e-nose) technology, gene expression profiling, and biomarker detection, hold promise for rapid and bedside diagnostics but require further validation to establish clinical applicability. Expert Opinion: Integrating molecular, metagenomic, biomarker-associated, and traditional diagnostics is essential for overcoming limitations. Continued technological refinements and cost reductions will enable broader clinical implementation. These innovations promise to enhance diagnostic accuracy, facilitate targeted therapy, and improve patient outcomes while contributing to global efforts to mitigate antimicrobial resistance. Full article

The human microbiome, a complex ecosystem of microorganisms residing in and on the body, plays a pivotal role in the regulation of a wide range of physiological processes, including digestion, immune responses, and metabolic functions. In recent years, the rapidly growing field of microbiome-driven therapeutics has garnered significant attention owing to its potential to revolutionize healthcare. This review explores the evolving landscape of microbiome-based therapies, with a particular focus on the gut microbiome and its implications for both gut health and precision medicine. We highlight recent advances in understanding how microbial communities influence disease pathogenesis and treatment outcomes, spanning conditions such as inflammatory bowel disease (IBD), metabolic disorders, neurological diseases, and even cancer. This article also discusses emerging therapeutic strategies, including probiotics, prebiotics, fecal microbiota transplantation (FMT), and microbial-based drugs, as well as the challenges associated with their clinical implementation. Additionally, we examined how the integration of microbiome profiling and metagenomic data is advancing the field of precision medicine, paving the way for personalized and effective treatments. This review serves as a comprehensive resource that synthesizes current knowledge, identifies key gaps in microbiome research, and offers insights into the future direction of microbiome-driven therapeutics, thus providing a valuable framework for clinicians, researchers, and policymakers seeking to harness the potential of microbiomes to advance personalized healthcare solutions. Full article

The climate change-associated abnormal weather patterns negatively influences the productivity and performance of farm animals. Heat stress is the major detrimental factor hampering production, causing substantial economic loss to the livestock industry. Therefore, it is important to identify heat-tolerant breeds that can survive and produce optimally in any given environment. To achieve this goal, a clearer understanding of the genetic differences and the underlying molecular mechanisms associated with climate change impacts and heat tolerance are a prerequisite. Adopting next-generation biotechnological and statistical tools like whole transcriptome analysis, whole metagenome sequencing, bisulphite sequencing, genome-wide association studies (GWAS), and selection signatures provides an opportunity to achieve this goal. Through these techniques, it is possible to identify permanent genetic markers for heat tolerance, and by incorporating those markers in marker-assisted breeding selection, it is possible to achieve the target of breeding for heat tolerance in livestock. This review gives an overview of the recent advancements in assessing heat tolerance in livestock using such ‘omics’ approaches and statistical models. The salient findings from this research highlighted several candidate biomarkers that have the potential to be incorporated into future heat-tolerance studies. Such approaches could revolutionise livestock production in the changing climate scenario and support the food demands of the growing human population. Full article

Commercially cultivated Prunus species are commonly grown in adjacent or mixed orchards and can be infected with unique or commonly shared viruses. Apple (Malus domestica), another member of the Rosacea and distantly related to Prunus, can share the same growing regions and common pathogens. Pollen can be a major route for virus transmission, and analysis of the pollen virome in tree fruit orchards can provide insights into these virus pathogen complexes from mixed production sites. Commercial honey bee (Apis mellifera) pollination is essential for improved fruit sets and yields in tree fruit production systems. To better understand the pollen-associated virome in tree fruits, metagenomics-based detection of plant viruses was employed on bee and pollen samples collected at four time points during the peak bloom period of apricot, cherry, peach, and apple trees at one orchard site. Twenty-one unique viruses were detected in samples collected during tree fruit blooms, including prune dwarf virus (PDV) and prunus necrotic ringspot virus (PNRSV) (Genus Ilarvirus, family Bromoviridae), Secoviridae family members tomato ringspot virus (genus Nepovirus), tobacco ringspot virus (genus Nepovirus), prunus virus F (genus Fabavirus), and Betaflexiviridae family member cherry virus A (CVA; genus Capillovirus). Viruses were also identified in composite leaf and flower samples to compare the pollen virome with the virome associated with vegetative tissues. At all four time points, a greater diversity of viruses was detected in the bee and pollen samples. Finally, the nucleotide sequence diversity of the coat protein regions of CVA, PDV, and PNRSV was profiled from this site, demonstrating a wide range of sequence diversity in pollen samples from this site. These results demonstrate the benefits of area-wide monitoring through bee pollination activities and provide new insights into the diversity of viruses in tree fruit pollination ecosystems. Full article

While considerable progress has been made in understanding the complex relationships between gut microbiomes and their hosts, especially in mammals and humans, the functions of these microbial communities in avian species remain largely unexplored. This gap in knowledge is particularly notable, given the critical roles gut microbiomes are known to play in facilitating crucial physiological functions, such as digestion, nutrient absorption, and immune system development. Corvidae birds are omnivorous and widely distributed across various habitats, exhibiting strong adaptability and often displaying the traits of accompanying humans. However, to date, information on species composition, sequenced genomes, and functional characteristics of crow gut microbes is lacking. Herein, we constructed the first relatively comprehensive crows gut microbial gene catalog (2.74 million genes) and 195 high-quality and medium-quality metagenome-assembled genomes using 53 metagenomic samples from five typical crow species (Pyrrhocorax pyrrhocorax, Corvus dauuricus, Corvus frugilegus, Corvus macrorhynchos, and Corvus corax) on the Qinghai–Tibetan Plateau. The species composition of gut microbiota at the phylum and genus levels was revealed for these five crow species. Simultaneously, numerous types of prevalent pathogenic bacteria were identified, indicating the potential of these crows to transmit diseases within the local community. At the functional level, we annotated a total of 356 KEGG functional pathways, six CAZyme categories, and 3607 virulence factor genes in the gut microbiomes of the crows. The gut microbiota of five distinct crow species underwent a comparative analysis, which uncovered significant differences in their composition, diversity, and functional structures. Over 36% of MAGs showed no overlap with existing databases, suggesting they might represent new species. Consequently, these findings enriched the dataset of microbial genomes associated with crows’ digestive systems. Overall, this study offers crucial baseline information regarding the gut microbial gene catalog and genomes in crows, potentially aiding microbiome-based research, as well as an evaluation of the health risks to humans from the bacterial pathogens transmitted by wild birds. Full article

Cabbage (Brassica oleracea), a crop of major economic importance worldwide, is affected by numerous diseases, which are caused by a wide range of microorganisms, including fungi, oomycetes, bacteria, and viruses, which lead to important losses in yield and quality. The increasing availability of reference genomes of plant-associated microbes together with recent advances in metagenomic approaches provide new opportunities to identify microbes linked to distinct symptomatology in Brassica leaves. In this study, shotgun metagenomics was used to investigate the microbial community in leaves of B. oleracea plants from agricultural farmlands. Compared with conventional techniques based on culture-based methods, whole-genome shotgun sequencing allows the reliable identification of the microbial population inhabiting a plant tissue at the species level. Asymptomatic and symptomatic leaves showing different disease symptoms were examined. In the asymptomatic leaves, Xanthomonas species were the most abundant taxa. The relative abundance of bacterial and fungal communities varied depending on disease symptoms on the leaf. The microbiome of the leaves showing mild to severe levels of disease was enriched in bacterial populations (Sphingomonas, Methylobacterium, Paracoccus) and to a lesser degree in some fungal taxa, such as Alternaria and Colletotrichum (e.g., in leaves with high levels of necrotic lesions). Sclerotinia species were highly abundant in severely damaged leaves (S. sclerotium, S. trifolium, S. bolearis), followed by Botrytis species. The common and specific bacterial and fungal species associated to disease symptoms were identified. Finally, the analysis of the gene functions in the metagenomic data revealed enrichment in carbohydrate-active enzymes potentially involved in pathogenicity, whose distribution also varied among disease severity groups. Understanding the B. oleracea leaf microbiome in agricultural ecosystems will pave the way for the efficient management of diseases in this crop. Full article