Search Results (248)

Intercropping is an eco-friendly, sustainable agricultural model that significantly improves yield stability, nutrient use efficiency, and soil health through spatiotemporal niche complementarity, increases biodiversity, and improves soil health. Water and nitrogen play crucial roles in limiting and regulating efficient resource utilization and ecological sustainability in intercropping systems. Synchronizing water and nitrogen inputs to match crop demands optimizes the spatiotemporal distribution of these resources, alleviates interspecific competition, and promotes mutualistic interactions, which significantly impacts crop growth, yield, and soil environment. This paper reviews the mechanisms of intercropping and water–nitrogen coupling regulation, aligning water and nitrogen supply with crop growth patterns, spatial configuration parameters, irrigation management techniques, and environmental climate change, and explores the response mechanisms of water–nitrogen coupling on crop growth, yield, and soil environmental adaptation. It can provide some references for researchers, extension agents, and policymakers. Research indicates that water–nitrogen coupling can enhance photosynthetic efficiency, promote root development, optimize nutrient uptake, and improve soil water dynamics, nitrogen cycling, and microbial community structures. Intercropping enhances the climate resilience of agricultural systems by leveraging species complementarity for resource utilization, strengthening ecosystem stability, and improving buffering capacity against climate change impacts such as extreme precipitation and temperature fluctuations. Future studies should further elucidate the differential effect of water–nitrogen coupling across regions and climatic conditions, focusing on multidimensional integrated administration strategies. Combining precision agriculture technologies and climate change predictions facilitates the development of more adaptive water–nitrogen coupling models to provide theoretical support and technical guarantees for sustainable agriculture. Full article

Due to limited land resources and traditional farming practices, continuous cassava cropping is common in China. This practice leads to soil degradation, including reduced fertility, imbalanced microbial communities, and lower crop yields. In this study, we investigated the impacts of continuous cassava cropping (CC) and cassava–maize rotation (RC) systems on soil physicochemical properties, microbial community composition, and functional gene abundance related to carbon and nitrogen cycling. The RC system consists of a five-year rotation cycle: cassava is planted in the first year, followed by two consecutive years of maize, and then, cassava is planted again in the last two years. The soil type is classified as Haplic Acrisols with a clay loam texture in this research. Soil samples from both cropping systems were analyzed for physicochemical properties and enzyme activities, and the results showed significant decreases in soil pH, available nitrogen, available phosphorus, and available potassium in CC. Using metagenomic sequencing, 1,280,928 and 1,224,958 unigenes were identified under RC and CC, respectively, with differences in microbial taxonomic and functional profiles. Bacteria accounted for 89.257% of the soil community in RC, whereas the proportion was 88.72% in CC. The proportions of eukaryota and viruses in RC were 0.031% and 0.006%, respectively; in contrast, their proportions were 0.04% and 0.02% in CC, respectively. Cassava–maize rotation promoted the metabolic activities of soil microbes, leading to a significant enhancement in functional genes related to nitrogen and carbon cycling, such as nasA, nasD, nrtC, coxA, porA, and frdA. This shows that microbial activity and nutrient cycling improved in the crop rotation system. Thus, these findings highlight the importance of crop rotation for maintaining soil health, enhancing microbial functions, and improving sustainable cassava production. This study provides valuable insights into the management of cassava agroecosystems and the mitigation of the adverse effects of continuous cropping. Full article

The environmental burden of conventional plastics has sparked interest in sustainable alternatives such as polyhydroxyalkanoates (PHAs). However, despite ample research in bioprocess development and the use of inexpensive waste streams, production costs remain a barrier to widespread commercialization. Complementary to this, genetic engineering offers another avenue for improved productivity. Cupriavidus necator stands out as a model host for PHA production due to its substrate flexibility, high intracellular polymer accumulation, and tractability to genetic modification. This review delves into metabolic engineering strategies that have been developed to enhance the production of poly(3-hydroxybutyrate) (PHB) and related copolymers in C. necator. Strategies include the optimization of central carbon flux, redox and cofactor balancing, adaptation to oxygen-limiting conditions, and fine-tuning of granule-associated protein expression and the regulatory network. This is followed by outlining engineered pathways improving the synthesis of PHB copolymers, PHBV, PHBHHx, and other emerging variants, emphasizing genetic modifications enabling biosynthesis based on unrelated single-carbon sources. Among these, enzyme engineering strategies and the establishment of novel artificial pathways are widely discussed. In particular, this review offers a comprehensive overview of promising engineering strategies, serving as a resource for future strain development and positioning C. necator as a valuable microbial chassis for biopolymer production at an industrial scale. Full article

Cold seep ecosystems harbor unique microbial communities with potential for producing secondary metabolites. However, the metabolic potential of cold seep microorganisms in the South China Sea remains under-recognized. This study employed both culture-dependent and culture-independent approaches, including 16S rRNA amplicon sequencing and metagenomics, to investigate microbial communities and their potential for secondary metabolite production in the South China Sea cold seep. The results indicate microbial composition varied little between two non-reductive sediments but differed significantly from the reductive sediment, primarily due to Planctomycetes and Actinobacteria. Predicting the Secondary Metabolism Potential using Amplicon (PSMPA) predictions revealed 115 strains encoding more than 10 biosynthetic gene clusters (BGCs), with lower BGC abundance in reductive sediment. Culture-dependent studies showed Firmicutes as the dominant cultivable phylum, with strains from shallow samples encoding fewer BGCs. Metagenomic data confirmed distinct microbial compositions and BGC distributions across sediment types, with cold seep type having a stronger influence than geographic location. Certain BGCs showed strong correlations with sediment depth, reflecting microbial adaptation to nutrient-limited environments. This study provides a comprehensive analysis of the metabolic capabilities of South China Sea cold seep microorganisms and reveals key factors influencing their secondary metabolic potential, offering valuable insights for the efficient exploration of cold seep biological resources. Full article

The role of rhizosphere bacteria in facilitating plant invasion is increasingly acknowledged, yet the influence of specific microbial functional traits remains insufficiently understood. This study addresses this gap by isolating two bacterial strains, Bacillus sp. ScRB44 and Pseudomonas sp. ScRB22, from the rhizosphere of the invasive weed Solidago canadensis. We assessed their nitrogen utilization capacity and indoleacetic acid (IAA) production capabilities to evaluate their ecological functions. Our three-stage experimental design encompassed strain promotion, nutrient stress, and competition phases. Bacillus sp. ScRB44 demonstrated robust IAA production and significantly improved the nitrogen utilization efficiency, significantly enhancing S. canadensis growth, especially under nutrient-poor conditions, and promoting a shift in biomass allocation toward the roots, thereby conferring a competitive advantage over native species. Conversely, Pseudomonas sp. ScRB22 exhibited limited functional activity and a negligible impact on plant performance. These findings underscore that the ecological impact of rhizosphere bacteria on invasive weeds is closely linked to their specific growth-promoting functions. By enhancing stress adaptation and optimizing resource allocation, certain microorganisms may facilitate the establishment of invasive weeds in adverse environments. This study highlights the significance of microbial functional traits in invasion ecology and suggests novel approaches for microbiome-based invasive weed management, with potential applications in agricultural soil health improvement and ecological restoration. Full article

The dramatic increase in urban construction waste poses severe environmental challenges. Utilizing waste concrete to produce recycled aggregates (RA) for manufacturing recycled concrete (RC) represents an effective strategy for resource utilization. However, inherent defects in RA, such as high porosity, microcracks, and adherent old mortar layers, lead to significant performance degradation of the resulting RC, limiting its widespread application. Traditional methods for enhancing RA often suffer from limitations, including high energy consumption, increased costs, or the introduction of new pollutants. MICP offers an innovative approach for enhancing RC performance. This technique employs the metabolic activity of specific microorganisms to induce the formation of a three-dimensionally interwoven calcium carbonate gel network within the pores and on the surface of RA. This gel network can improve the inherent defects of RA, thereby enhancing the performance of RC. Compared to conventional techniques, this approach demonstrates significant environmental benefits and enhances concrete compressive strength by 5–30%. Furthermore, embedding mineralizing microbial spores within the pores of RA enables the production of self-healing RC. This review systematically explores recent research advances in microbial mineral gel network for improving RC performance. It begins by delineating the fundamental mechanisms underlying microbial mineralization, detailing the key biochemical reactions driving the formation of calcium carbonate (CaCO₃) gel, and introducing the common types of microorganisms involved. Subsequently, it critically discusses the key environmental factors influencing the effectiveness of MICP treatment on RA and strategies for their optimization. The analysis focuses on the enhancement of critical mechanical properties of RC achieved through MICP treatment, elucidating the underlying strengthening mechanisms at the microscale. Furthermore, the review synthesizes findings on the self-healing efficiency of MICP-based RC, including such metrics as crack width healing ratio, permeability recovery, and restoration of mechanical properties. Key factors influencing self-healing effectiveness are also discussed. Finally, building upon the current research landscape, the review provides perspectives on future research directions for advancing microbial mineralization gel techniques to enhance RC performance, offering a theoretical reference for translating this technology into practical engineering applications. Full article

Elevational gradients in temperature, moisture, and vegetation strongly influence soil nutrient content and stoichiometry in mountainous regions. However, exactly how total, microbial, and enzymatic carbon (C), nitrogen (N), and phosphorus (P) stoichiometry vary with elevation in karst peak-cluster depressions remains poorly understood. To address this, we studied soil total, microbial, and enzymatic C:N:P stoichiometry in seasonal rainforests within karst peak-cluster depressions in southwestern China at different elevations (200, 300, 400, and 500 m asl) and depths (0–20 and 20–40 cm). We found that soil organic carbon (SOC), total nitrogen (TN), and the C:P and N:P ratios increased significantly with elevation, whereas total phosphorus (TP) decreased. Microbial phosphorus (MBP) also declined with elevation, while the microbial N:P ratio rose. Activities of nitrogen- (β-N-acetylglucosaminidase and L-leucine aminopeptidase combined) and phosphorus-related enzymes (alkaline phosphatase) increased markedly with elevation, suggesting potential phosphorus limitation for plant growth at higher elevations. Our results suggest that total, microbial, and enzymatic soil stoichiometry are collectively shaped by topography and soil physicochemical properties, with elevation, pH, and exchangeable calcium (ECa) acting as the key drivers. Microbial stoichiometry exhibited positive interactions with soil stoichiometry, while enzymatic stoichiometry did not fully conform to the expectations of resource allocation theory, likely due to the functional specificity of phosphatase. Overall, these findings enhance our understanding of C–N–P biogeochemical coupling in karst ecosystems, highlight potential nutrient limitations, and provide a scientific basis for sustainable forest management in tropical karst regions. Full article

The coastal zone presents complex hydrodynamic interactions among inland groundwater, reservoir water, and intruding seawater, with important implications for ecosystem functioning and water quality. However, the relative roles of hydraulic connectivity and seawater-driven salinity gradients in shaping microbial communities at the aquifer–reservoir interface remain unclear. Here, we integrated hydrochemical analyses with high-throughput 16S rRNA gene sequencing to investigate bacterial community composition, assembly processes, and co-occurrence network patterns across groundwater_in (entering the reservoir), groundwater_out (exiting the reservoir), and reservoir water in a coastal system. Our findings reveal that seawater intrusion exerts a stronger influence on groundwater_out, leading to distinct chemical profiles and salinity-driven environmental filtering, whereas hydraulic connectivity promotes greater microbial similarity between groundwater_in and reservoir water. Groundwater samples exhibited higher alpha and beta diversity compared to the reservoir, with dominant taxa such as Comamonadaceae, Flavobacteriaceae, and Rhodobacteraceae serving as indicators of seawater intrusion. Community assembly analyses showed that homogeneous selection predominated, especially under strong salinity gradients, while dispersal limitation and spatial distance also contributed in areas of reduced connectivity. Key chemical factors, including TDS, Na⁺, Cl⁻, Mg²⁺, and K⁺, strongly shaped groundwater communities. Additionally, groundwater bacterial networks were more complex and robust than those in reservoir water, suggesting enhanced resilience to salinity stress. Collectively, this study demonstrates that salinity gradients can override the effects of hydraulic connectivity in structuring bacterial communities and their networks at coastal interfaces. Our findings provide novel microbial insights relevant for understanding biogeochemical processes and support the use of microbial indicators for more sensitive monitoring and management of coastal groundwater resources. Full article

This study presents an integrated approach to sustainable soil and crop management by evaluating the individual and combined effects of cow manure (CM), rice husk biochar (RHB), and potassium humate (KH)—three underutilized, low-cost organic amendments derived from agricultural byproducts. Uniquely, it investigates how these amendments simultaneously affect soil physical and chemical properties, plant growth, and the accumulation of bioactive compounds in sunflower sprouts, thereby linking soil health to crop nutritional quality. The application of 2% w/w KH alone resulted in the greatest increases in macroaggregation (+0.51), soil pH (from 6.8 to 8.6), and electrical conductivity (+298%). The combination of 1% w/w CM and 2% KH led to the highest increases in soil organic carbon (OC, +62.9%) and soil respiration (+56.4%). Nitrate and available phosphorus (P) peaked with 3% w/w RHB + 2% KH (+120%) and 1% w/w CM + 0.5% KH (+35.5%), respectively. For plant traits, 0.5% w/w KH increased the total leaf area by 61.9%, while 1% w/w CM enhanced shoot and root biomass by 60.8% and 79.0%, respectively. In contrast, 2% w/w KH reduced chlorophyll content (−43.6%). Regarding bioactive compounds, the highest total phenolic content (TPC) was observed with 1% w/w KH (+21.9%), while the strongest DPPH antioxidant activity was found under 1% w/w CM + 1% w/w KH (+72.6%). A correlation analysis revealed that biomass production and secondary metabolite accumulation are shaped by trade-offs arising from resource allocation under stress or nutrient limitations. Potassium, P, soil microbial respiration, and OC emerged as key integrators connecting soil structure, fertility, and plant metabolic responses. Overall, the combination of 1% w/w CM with 0.5–1% w/w KH proved to be the most effective strategy under the tested conditions. Full article

With the global rise in antimicrobial resistance (AMR), rapid and reliable microbial diagnostics have become more critical than ever. Traditional culture-based and molecular diagnostic techniques often fall short in terms of speed, cost-efficiency, or scalability, particularly in resource-limited settings. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI–TOF MS) has emerged as a transformative tool in clinical microbiology. Its unparalleled speed and accuracy in microbial identification, along with expanding applications in AMR profiling, make it a leading candidate for next-generation diagnostic workflows. This review aims to provide a comprehensive update on recent advances in MALDI–TOF MS, focusing on its technological evolution, clinical applications, and future potential in microbial diagnostics and resistance detection. We conducted a critical synthesis of peer-reviewed literature published over the last decade, with emphasis on innovations in sample preparation, instrumentation, data interpretation, and clinical integration. Key developments in AMR detection, including growth-based assays, resistance biomarker profiling, and machine learning-driven spectral analysis, are discussed. MALDI–TOF MS is increasingly deployed not only in clinical laboratories but also in environmental surveillance, food safety, and military biodefense. Despite challenges such as database variability and limited access in low-income regions, it remains a cornerstone of modern microbial diagnostics and holds promise for future integration into global AMR surveillance systems. Full article

Soy molasses, a byproduct of soy protein concentrate production, offers potential as a substrate for biotechnological applications due to its rich composition of carbohydrates, proteins, lipids, and bioactive compounds. Despite this, it remains underutilized, often relegated to low-value applications such as animal feed or waste, largely due to variability in its composition, the presence of microbial inhibitors, and limited industrial awareness of its potential. This review explores the biotechnological strategies for valorizing soy molasses, focusing on its chemical and physical properties, potential applications, and the challenges associated with its use. Its high carbohydrate content supports its utilization in producing biofuels, organic acids, and polyhydroxyalkanoates (PHA), addressing the global demand for sustainable energy and materials while costing approximately 20% of the value of conventional carbohydrate sources. Additionally, bioactive compounds have extended applications to nutraceuticals and cosmetics, while proteins and lipids enable enzyme and biosurfactant production. However, challenges such as variability in composition, the presence of inhibitory compounds, and scalability issues require innovative approaches, including pre-treatment methods and strain engineering. By integrating soy molasses into a circular bioeconomy framework, industries can reduce waste, lower their carbon footprint, valorize agro-industrial residues, and generate economic value. This review underscores the untapped potential of soy molasses as a versatile, sustainable resource, while highlighting the need for continued advancements to transform it into a key player in industrial biotechnology. Full article

Outbreaks of infectious diseases contribute significantly to morbidity and mortality in resource-limited settings, yet the capacity to identify their etiology remains limited. We aimed to characterize microbes and antimicrobial resistance (AMR) genes in Tanzanian children affected by an acute febrile illness (AFI) outbreak using metagenomic next-generation sequencing (mNGS). A cross-sectional study was conducted on archived blood samples from children who presented with AFI between 2018 and 2019. Total nucleic acids were extracted from 200 µL of blood, and complementary DNA (cDNA), along with enriched pathogenic DNA, was sequenced using the Illumina MiSeq platform. mNGS data were analyzed using CZ-ID Illumina mNGS bioinformatics pipeline v7.0. Results were obtained from 25 participants (mean age: 11.6 years; SD ± 5), of whom 36% had a moderate to high-grade fever. The following five potential microbial causes of AFI were identified: Escherichia coli (n = 19), Paraclostridium bifermentans (n = 2), Pegivirus C (n = 2), Shigella flexneri (n = 1) and Pseudomonas fluorescens (n = 1), with E. coli being the most prevalent. Twelve AMR genes were detected, including mdtC, acrF, mdtF, and emrB. E. coli harbored most of the AMR genes previously associated with resistance to commonly used antibiotics. mNGS offers a promising complementary approach to conventional diagnostics for identifying pathogens and AMR profiles in vulnerable populations. Full article

Fed-batch cultivation is a widely used strategy for microbial lipid production, offering flexibility in nutrient control and the potential for high lipid productivity. However, optimizing feeding strategies remains a complex challenge, as it depends on multiple factors, including strain-specific metabolism and process limitations. In this study, we developed a computational framework based on dynamic flux balance analysis and small-scale metabolic models to evaluate and optimize lipid production in Rhodosporidium toruloides strains. We proposed equations to estimate both the carbon and energy source mass feed rate ($F_{in}·s_r$) and its concentration in the feed ($s_r$) based on lipid accumulation targets, and defined minimum feeding flow rate ($F_{in}$) according to process duration. We then assessed the impact of these parameters on commonly used bioprocess metrics—lipid yield, titer, productivity, and intracellular accumulation—across wild-type and engineered strains. Our results showed that the selection of $F_{in}·s_r$ was strongly strain-dependent and significantly influenced strain performance. Moreover, for a given $F_{in}·s_r$, the specific values of $s_r$, and the resulting $F_{in}$, had distinct and non-equivalent effects on performance metrics. This methodology enables the rational pre-selection of feeding strategies and strains, improving resource efficiency and reducing the probability of failed experiments. Full article

As a globally critical carbon reservoir, the response mechanism of wetland ecosystems to climate change on the Qinghai–Tibet Plateau (QTP) has attracted significant scientific scrutiny. This study investigated the temperature sensitivity of cbbL-harboring carbon-sequestering microbial communities and their coupling with carbon–nitrogen cycle dynamics through a simulated field warming experiment conducted in the Wayan Mountains’ river source wetland in the northeastern QTP. Key findings revealed that warming markedly elevated Alpha diversity (ACE and Chao1 indices), whereas Shannon and Simpson indices remained stable, indicating that temperature increases primarily altered community composition by enhancing species richness rather than evenness. Taxonomic analysis demonstrated significant increases in the relative abundances of Cyanobacteria and Actinobacteria, while Proteobacteria retained dominance but exhibited reduced relative abundance. At the genus level, Thioflexothrix, Ferrithrix, and Rhodospirillum dominated the community, with Thioflexothrix and Ferrithrix showing warming-induced abundance increments. Functional predictions indicated that warming preferentially stimulated heterotrophic and photoheterotrophic functional guilds. Soil physicochemical analyses further revealed warming-driven increases in nitrate nitrogen (NN), total carbon (TC), and total nitrogen (TN), concurrent with decreased soil moisture. Redundancy analysis identified TC as the predominant determinant of microbial community structure (followed by TN > NN), while pH and ammonium nitrogen (AN) exerted comparatively limited influence. Strong positive correlations between microbial communities and carbon/nitrogen indicators suggested that enhanced carbon–nitrogen resource availability served as the central driver of community succession. These findings elucidate the temperature-responsive mechanisms of cbbL-type carbon-sequestering microorganisms in alpine wetlands, offering critical insights for the adaptive management of carbon cycling in high-altitude ecosystems and advancing strategies toward achieving carbon neutrality goals. Full article

Due to its high digestibility, rich nutrient profile, and potential probiotic content, goat milk is an essential nutritional resource, particularly for individuals with cow milk allergies. This review summarises the current state of microbial diversity in goat milk, emphasising the implications for quality, safety, and probiotic potential. This systematic review adhered to PRISMA guidelines, conducting a comprehensive literature search across PubMed, ScienceDirect, and Google Scholar using keywords related to microbial profiling in goat milk. The inclusion criteria targeted English-language studies from 2000 to 2025 that utilised high-throughput or next-generation sequencing methods. Out of 126 articles screened, 84 met the eligibility criteria. The extracted data focused on microbial diversity, profiling techniques, and their respective strengths and limitations in evaluating probiotic potential and spoilage risks. The review addresses the challenges linked to microbial spoilage and the composition and functional roles of microbial communities in goat milk. With species such as Bacillus and Pseudomonas playing crucial roles in fermentation and spoilage, key findings emphasise the prevalence of microbial phyla, including Proteobacteria, Firmicutes, and Actinobacteria in goat milk. The review also explores the probiotic potential of the goat milk microbiota, highlighting the health benefits associated with strains such as Lactobacillus and Bifidobacterium. Significant discoveries underline the necessity for advanced multi-omics techniques to thoroughly define microbial ecosystems and the substantial gaps in breed-specific microbiota research. Important findings illustrate the need for enhanced multi-omics techniques, given the challenges of host RNA and protein interference, low microbial biomass, and limited goat-specific reference databases, for optimising probiotic development, spoilage prevention strategies, and integrating metagenomics, metabolomics, metaproteomics, and metatranscriptomics to improve milk quality and safety as some of the future research objectives. This study emphasises the importance of understanding goat milk microbiology to advance dairy science and enhance human health. Full article