Search Results (306)

Bacteriophages have been widely investigated as a promising treatment of food, medical equipment, and humans colonized by antibiotic-resistant bacteria. Phages pose particular interest in combating those bacteria which form biofilms, such as the medically important human pathogen Pseudomonas aeruginosa and several plant pathogens, including P. syringae. In an undergraduate lab course, P. putida was used as the host to isolate novel anti-pseudomonal bacteriophages. Environmental samples of soil and water were collected, and purified phage isolates were obtained. After Illumina sequencing, genomes of these phages were assembled de novo and annotated. Assembled genomes were compared with known genomes in the literature and GenBank to identify taxonomic relations and to refine their functional annotations. The thirteen phages described are sipho-, myo-, and podoviruses in several families of Caudoviricetes, spanning several novel genera, with genomes ranging from 40,000 to 96,000 bp. One phage (DDSR119) is unique and is the first reported P. putida siphovirus. The remaining 12 can be clustered into four distinct groups. Six are highly related to each other and to previously described Autotranscriptaviridae phages: Waldo5, PlaquesPlease, and Laces98 all belong to the Waldovirus genus, whereas Stalingrad, Bosely, and Stamos belong to the Troedvirus genus. Zuri was previously classified as the founding member of a new genus Zurivirus within the family Schitoviridae. Ebordelon and Holyagarpour each represent different species within Zurivirus, whereas Meara is a more distantly related member of the Schitoviridae. Dolphis and Jeremy are similar enough to form a genus but have only a few distant relatives among sequenced phages and are notable for being temperate. We identified the lysis cassettes in all 13 phages, compared tail spike structures, and found auxiliary metabolic genes in several. Studies like these, which isolate and characterize infectious virions, enable the identification of novel proteins and molecular systems and also provide the raw materials for further study, evaluation, and manipulation of phage proteins and their hosts. Full article

Cadmium (Cd), a pervasive and highly phytotoxic metal pollutant, poses severe threats to agricultural productivity, ecosystem stability, and human health through its entry into the food chain. Plants have evolved intricate defense mechanisms, among which the strategic manipulation of nutrient elements emerges as a critical physiological and biochemical strategy for mitigating Cd stress. This comprehensive review delves deeply into the multifaceted roles of essential macronutrient elements (nitrogen, phosphorus, potassium, calcium, magnesium, sulfur), essential micronutrient elements (zinc, iron, manganese, copper) and non-essential beneficial elements (silicon, selenium) in modulating plant responses to Cd toxicity. We meticulously dissect the physiological, biochemical, and molecular underpinnings of how these nutrients influence Cd bioavailability in the rhizosphere, Cd uptake and translocation pathways, sequestration and compartmentalization within plant tissues, and the activation of antioxidant defense systems. Nutrient elements exert their influence through diverse mechanisms: competing with Cd for root uptake transporters, promoting the synthesis of complexes that reduce Cd mobility, stabilizing cell walls and plasma membranes to restrict apoplastic flow and symplastic influx, modulating redox homeostasis by enhancing antioxidant enzyme activities and non-enzymatic antioxidant pools, regulating signal transduction pathways, and influencing gene expression profiles related to metal transport, chelation, and detoxification. The complex interactions between nutrients themselves further shape the plant’s capacity to withstand Cd stress. Recent advances elucidating nutrient-mediated epigenetic regulation, microRNA involvement, and the role of nutrient-sensing signaling hubs in Cd responses are critically evaluated. Furthermore, we synthesize the practical implications of nutrient management strategies, including optimized fertilization regimes, selection of nutrient-efficient genotypes, and utilization of nutrient-enriched amendments, for enhancing phytoremediation efficiency and developing low-Cd-accumulating crops, thereby contributing to safer food production and environmental restoration in Cd-contaminated soils. The intricate interplay between plant nutritional status and Cd stress resilience underscores the necessity for a holistic, nutrient-centric approach in managing Cd toxicity in agroecosystems. Full article

Saline–alkali soils in arid regions are increasingly recognized as critical yet underrepresented components of the global carbon cycle. However, their CO₂ flux dynamics under warming remain poorly understood. In this study, we conducted controlled growth-chamber experiments using typical saline–alkali soils from the Taklamakan Desert, where temperature, soil moisture, and atmospheric CO₂ concentrations were systematically manipulated. We quantified how warming reshaped moisture–temperature interactions regulating soil CO₂ fluxes. The results revealed a pronounced diurnal variation pattern, characterized by daytime CO₂ release and nighttime uptake. Temperature was identified as the dominant driver (R² > 0.93, p < 0.001), whereas soil moisture primarily modulated flux intensity; at 0.8 cm³ cm⁻³, fluxes declined by up to 61% compared with the baseline. Warming enhanced the temperature–moisture synergy (−43%, p < 0.01) and simultaneously reduced baseline fluxes (−56%, p < 0.01). These shifts fundamentally altered the regulation of CO₂ flux dynamics. Our findings highlight the necessity of integrating salt dynamics and carbonate equilibria into multiphase reactive transport models to improve regional carbon sink assessments. Ultimately, this study refines estimates of the contribution of saline–alkali soils to the global “missing carbon sink” (~1.7 Pg C a⁻¹) and emphasizes their overlooked role in the Earth’s carbon budget under a warming climate. Full article

Zinc (Zn) deficiency affects over 30% of the global population, with the highest burdens in developing countries reliant on cereal-based diets. As a major dietary staple in regions such as Sub-Saharan Africa and Latin America, common bean (Phaseolus vulgaris L.) represents a promising vehicle for addressing hidden hunger. This review critically evaluates the efficacy of various strategies to enhance Zn concentration in common bean, ranging from agronomic to genetic manipulation, and proposes promising strategies for biofortifying common bean in developing countries that are resource- and technology-limited. Biofortification strategies include agronomic practices, conventional breeding, and genetic engineering, each with distinct strengths and limitations. Agronomic methods such as soil and foliar fertilization can rapidly increase micronutrient content, but they require recurrent costs and may not be sustainable for smallholders without subsidies. Genetic engineering, particularly transgenic approaches, can significantly boost Zn levels; however, regulatory hurdles, cost of production, and public acceptance remain significant obstacles to widespread adoption. Conventional breeding is secure and widely adopted, but is time-consuming and limited by genetic diversity, making it less precise and slower than genetic engineering. We argue for a context-specific and integrated biofortification framework that prioritizes agronomic interventions such as biofertilizer, seed priming, soil Zn application, and foliar Zn application as approaches for quick results. Moderate- to long-term progress towards a biofortified common bean can be achieved using conventional breeding methods by selecting for local germplasm that accumulates higher Zn amounts in grain. On the other hand, genetic engineering is best for rapid, targeted nutrient enhancement where genetic diversity is lacking, but faces regulatory and acceptance challenges. We recommend that policymakers prioritize frameworks that harmonize these approaches, improve communication and education regarding the benefits of biofortified crop produce, subsidize and strengthen biofortified seed systems, and promote soil health initiatives. Full article

Coffee Coffea arabica L. depends on abundantly distributed rainfall, and drought negatively impacts plant development, fruit production, bean quality, and, ultimately, beverage quality. Plant biotechnology by means of genetic manipulation and plant regeneration by the somatic embryogenic process is an alternative technology to overcome these problems. In the present work, we used the molecular approach of the Trehalase gene silencing to allow trehalose accumulation favoring plants surviving in extreme drought/salt environments. We used a cassette containing the antisense C. arabica L. Trehalase gene under the RD29 promoter from A. thaliana and the NOS terminator to genetically modify an embryogenic coffee C. arabica L. cv Typica line under osmotic stress supplemented with mannitol (0.3 M) and sorbitol (0.3 M). Osmotic stress-tolerant somatic embryos lines were recovered and regenerated into plants. Tolerant somatic embryo lines showed a higher rate of competence to induce secondary SE capacity and plants robustness. These lines showed a down-regulation of the Trehalase; accumulation of trehalose, sucrose, starch, and proline; higher photosynthetic rate; improved water-use efficiency; and appropriated vapor deficit pressure under soil conditions. A transcriptome analysis was performed from highly competent somatic embryogenic lines to understand the molecular mechanisms underlying osmotic-stress tolerance. From the up-regulated genes, a PPI network made by STRING v12.0 with high confidence (0.700) revealed the presence of the 10 modules: the cell cycle, chromatin remodeling, somatic embryogenesis, oxidative stress, generic transcription pathway, carbon metabolism, phenylpropanoid biosynthesis, trehalose biosynthesis, proline biosynthesis, and glycerolipid metabolism. Full article

In forest land reclamation, revegetation efforts often focus on restoring tree composition, while the recovery of the understory vegetation community is typically left to natural regeneration. This regeneration relies mainly on wind-dispersed seeds, ingress from adjacent intact forests, or seed emergence from stockpiled surface soils. We examined the growth and survival of nursery-propagated, field-planted native herbaceous forbs on a reclaimed industrial site where topsoil placement depth was varied to manipulate soil nutrient availability and levels of competing vegetation. A pre-emergent herbicide was applied to half of the standard topsoil plots to assess the impact of ruderal vegetation competition. We addressed the following two questions: (1) How does placed topsoil depth affect the growth and survival of native forbs? We hypothesized that deeper topsoil (higher nutrient availability) would enhance growth but reduce survival due to increased competition. (2) Does competing ruderal vegetation negatively affect survival and/or growth? We hypothesized that competition would reduce growth in all species, but that Canada goldenrod (Solidago canadensis L.) would show greater resilience due to its pioneering nature. The results showed that S. canadensis exhibited consistently high growth and survival across all topsoil treatments, confirming its competitive advantage. Showy aster (Eurybia conspicua (Lindl.) G.L.Nesom) survival remained high during no-topsoil and shallow-topsoil treatments, with reductions under standard-depth topsoil linked to increased competition. Spreading dogbane (Apocynum androsaemifolium L.) survival varied but tended to be higher in no-topsoil and shallow-topsoil conditions. These findings suggest that certain native forbs can thrive across a range of soil conditions, and that Canada goldenrod, in particular, is a strong candidate for revegetation programs where competition from ruderal vegetation is a concern. Full article

The growing demand for animal products exerts pressure on the livestock sector to increase production while minimizing its impact on the environment. The paper explored the impact of ruminant production systems on the environment and opportunities for enhancing production and environmental conservation. A comprehensive review of literature on livestock production, animal nutrition, and environmental conservation was conducted. The review shows that the challenges of ruminant production on the ecosystem are centered around greenhouse gas emissions, land degradation, and water and feed resources. However, manipulation of animal feeding strategies, rotational grazing, precision farming, and integration of crop-livestock systems have the potential to enhance feed efficiency, reduce waste, improve animal health, and nutrition and reduce nitrogen and methane gas emissions. This will also improve manure management, soil health, and biodiversity, which are essential in climate resilience building and resource management by farmers. Development of effective strategies for enhancing animal nutrition and ruminant production while conserving the ecosystem is important. Full article

Desert steppe ecosystems, characterized by water limitation and high sensitivity to global climate change and anthropogenic disturbance drivers, experience profound alterations in carbon (C) cycling processes driven by the multiplicative interactions among grassland grazing, altered precipitation regimes, and elevated atmospheric nitrogen deposition. However, how historical grazing legacies modulate ecosystem responses to concurrent changes in nitrogen deposition and precipitation regimes remains poorly resolved. To address this, we conducted a field experiment manipulating water and nitrogen addition across grazing intensities (no grazing, light grazing, moderate grazing, heavy grazing) in a Stipa breviflora desert steppe. Over three consecutive growing seasons (2015–2017), we continuously monitored net ecosystem CO₂ exchange (NEE), ecosystem respiration (ER), and gross ecosystem production (GEP) to quantify ecosystem CO₂ fluxes under these interacting global change drivers. Results revealed that water and nitrogen addition did not alter seasonal CO₂ flux dynamics across grazing intensities. Light grazing enhanced ecosystem C sink capacity, whereas heavy grazing reduced NEE and GEP, diminishing C sink strength. Water addition significantly increased CO₂ fluxes, strongly correlated with soil moisture. Nitrogen addition exerted a weak C source effect in a water-deficient year but enhanced the C sink in a water-rich year. Nitrogen plus water addition significantly boosted C sink potential, though this effect diminished along the grazing pressure gradient. Our findings demonstrate that the impacts of climate change on soil C fluxes in desert steppes are mediated by historical grazing intensity. Future manipulative experiments should explicitly incorporate grazing legacy effects, and integrate this factor into C models to generate reliable predictions of grassland C dynamics under global change scenarios. Full article

This study investigates the impact of environmental changes induced by systematic manipulation of flooding depth and breeding density on greenhouse gas emissions in the field-based giant rice–fish hybrid farming model. Compared with traditional agricultural practices, increasing cultured density in giant rice–fish co-cultivation significantly alleviated the adverse consequences of flooding on soil nutrient dynamics, microbial activity community structure, and greenhouse gas emissions. Relative to the traditional alternating wet and dry irrigation, the soil concentrations of ammonium, total nitrogen, and phosphate significantly increased. Cultured fish had significantly increased soil microbial biomass carbon, nitrogen, and phosphorus contents and improved soil β-glucosidase and aryl-sulfatase activates relative to flooding alone. Cultured fish increased the relative abundances of Actinobacteria, Nitrospirae, Planctomycetes, Verrucomicrobia, and Aminicenantes. An increasing cultured fish density reduced cumulative methane and nitrous oxide emissions and GWP (global warming potential). Relative to the continuous flooding throughout the growing period, cumulative methane emissions and GWP in the flooding with high-density cultured fish were reduced by 5.32% and 1.48%, respectively. Notably, this co-cultivation strategy has the potential to transform traditional practices for sustainable agriculture. Nevertheless, it is imperative to remain vigilant about the potential consequences of greenhouse gas emissions associated with these innovative practices. Continuous monitoring and refinement are essential to ensure the long-term sustainability and viability of this agricultural approach. Full article

Altered precipitation regimes, both in intensity and duration, can profoundly influence the structure and function of soil microbial communities, yet the patterns and drivers of these responses remain unclear across ecosystem types. Here, using data exclusively from 101 field experiments conducted in China (yielding 695 observations), we investigated the impacts of altered precipitation on soil microbial biomass, diversity, and enzymatic activity in forest and grassland ecosystems. Soil microbial biomass carbon (MBC) and nitrogen (MBN) increased in response to precipitation addition, particularly in grasslands, but they decreased under reduced precipitation, with the decline being more pronounced in forests. The magnitude and duration of precipitation manipulation significantly influenced these effects, with moderate and long-term changes producing divergent responses. Bacterial diversity was largely unaffected by all precipitation treatments, whereas fungal diversity decreased significantly under intense and short-term reductions in precipitation. Enzyme activities exhibited the following element-specific patterns: carbon- and phosphorus-cycling enzymes and antioxidant enzymes were suppressed by precipitation reduction, especially in grasslands, while nitrogen-cycling enzymes showed no consistent response. Moreover, microbial responses were significantly shaped by environmental factors, including mean annual temperature (MAT), mean annual precipitation (MAP), and elevation. Our region-specific analysis highlights precipitation-driven microbial dynamics across China’s diverse climatic and ecological conditions. These findings demonstrate that soil microbial communities respond asymmetrically to precipitation changes, with responses shaped by both ecosystem type and climatic context, underscoring the need to account for environmental heterogeneity when predicting belowground feedback to climate change. Full article

The improvement in yield in cultivar mixtures has been well established. Despite increasing knowledge of the improvement involving within-species diversification and resource use efficiency, little is known about the benefits arising from relatedness-mediated intraspecific interactions in cultivar mixtures. This study used a relatedness gradient of rice cultivars to test whether neighbor relatedness contributes to improvements in grain yields in cultivar mixtures. We experimentally demonstrated the grain yield of rice cultivar mixtures with varying genetic relatedness under both field and controlled conditions. As a result, a closely related cultivar mixture had increased grain yield compared to monoculture and distantly related mixtures by optimizing the root-to-shoot ratio and accelerating flowering. The benefits over monoculture were most pronounced when compared to the significant yield reductions observed in distantly related mixtures. The relatedness-mediated improvement in yields depended on soil volume and nitrogen use level, with effects attenuating under larger soil volumes or nitrogen deficiency. Furthermore, neighbor relatedness enhanced the richness and diversity of both bacterial and fungal communities in the rhizosphere soil, leading to a significant restructuring of the microbial community composition. These findings suggest that neighbor relatedness may improve the grain yield of rice cultivar mixtures. Beneficial plant–plant interactions may be generated by manipulating cultivar kinship within a crop species. A thorough understanding of kinship strategies in cultivar mixtures offers promising prospects for increasing crop production. Full article

Our study was conducted in the Valle Nuevo National Park and included four habitat classes: tussock grass (Sabapa), pine forest (Pinoc), broadleaf forest (Boslat), and agricultural ecosystem (Ecoag). We had two main objectives: to comparatively describe millipede communities and to determine the relationships between population density/diversity and soil physicochemical variables. The research was cross-sectional and non-manipulative, with a descriptive and correlational scope; sampling followed a stratified systematic design, with eight transects and 32 quadrats of 1 m², covering 21.7 km. We found a sandy loam soil with an extremely acidic pH. The highest population density of millipedes was recorded in Sabapa, and the lowest in Ecoag. The highest alpha diversity was shared between Boslat (Margalef = 1.72) and Pinoc (Shannon = 2.53); Sabapa and Boslat showed the highest Jaccard similarity (0.56). The null hypothesis test using the weighted Shannon index revealed a statistically significant difference in diversity between the Boslat–Sabapa and Pinoc–Sabapa pairs. Two of the species recorded highly significant indicator values (IndVal) for two habitat classes. We found significant correlations (p < 0.05) between various soil physicochemical variables and millipede density and diversity. Full article

Chaetomium globosum is a widely distributed fungal species recognized for its ability to produce a range of secondary metabolites. This fungus plays a significant ecological role by degrading organic matter and contributing to nutrient cycling in diverse ecosystems. In recent years, C. globosum has attracted considerable scientific interest due to its potential as a biocontrol agent [BCA] against a wide array of diseases in numerous plant species. While the precise mechanisms of C. globosum as a BCA remain poorly understood, interference competition through antibiosis is one of the key mechanisms. Moreover, C. globosum can enhance plant health by promoting nutrient availability, manipulating the rhizosphere microbiome, and inducing plant defense responses. The formulation of C. globosum for agricultural applications has been reported, which can significantly improve stability and efficacy under field conditions. However, despite significant advancements in omics and molecular biology technologies, the biology of C. globosum is understudied. Enhanced research into the genetics and functional genomics of C. globosum could pave the way for its applications in sustainable agriculture. This review summarizes the role of C. globosum as a BCA, focusing on its underlying mechanisms such as genomics and transcriptomics, and the effects of C. globosum application on soil health and the rhizosphere microbiome. Full article

Utilizing straw feed is an effective strategy to optimize straw resource utilization by incorporating microbial degradation agents to expedite lignocellulose breakdown and enhance feed efficiency. Lignocellulose-degrading species and microbial communities are present in various Earth ecosystems, including the rumen of ruminants, insect digestive tracts, forest soil, and microbial populations in papermaking processes. The rumen of ruminants harbors a diverse range of microbial species, making it a promising source of lignocellulose-degrading microorganisms. Exploring alternative systems like insect intestines and forest soil is essential for future research. Current studies primarily rely on traditional microbial isolation techniques to identify lignocellulose-degrading strains, underscoring the necessity to transition to utilizing microbial culturomics and genome-editing technologies for discovering and manipulating cellulose-degrading microbes. This review provides an overview of lignocellulose-degrading microbial communities from diverse environments, encompassing bacterial and fungal populations. It also delves into the use of metagenomic, metatranscriptomic, and metaproteomic approaches to pinpoint highly efficient cellulase genes, along with the application of genome-editing tools for engineering lignocellulose-degrading microorganisms. The primary objective of this review is to offer insights for further exploration of potential lignocellulose-degrading microbial resources and high-performance cellulase genes to enhance roughage utilization in ruminant rumen ecosystems. Full article

In the context of China’s ecosystem facing a high intensity of nitrogen loads, carbon–nitrogen interactions are receiving increasing attention. Physical protection by soil aggregates is critical for soil carbon and nitrogen sequestration in terrestrial ecosystems; however, there is currently limited information on how nitrogen addition influences carbon and nitrogen dynamics across different stages of forest ageing. Herein, a field nitrogen manipulation experiment over 6 years was established in subtropical forests (46, 78, and about 200 years old) in China. Aggregate fractions and stable isotope analyses were used to assess the effects of nitrogen addition. The results show that forest soil was dominated by macroaggregates, and these increased with forest ageing (p > 0.05). The macroaggregates’ carbon content decreased with forest ageing (p > 0.05), while the macroaggregates’ nitrogen content was highest in the 200-year-old forest. Nitrogen addition increased the aggregates’ carbon and nitrogen concentrations in the 46- and 200-year-old forests. The macroaggregates, under nitrogen addition in the 78- and 200-year-old forests, were relatively weak, while forest age and nitrogen addition mainly affected macroaggregate carbon and nitrogen concentrations to promote their carbon and nitrogen storage, and the macroaggregates were the main storage unit for fixing and protecting new carbon in soils. Nitrogen addition increased the macroaggregates’ δ¹³C abundance in the 78- and 200-year-old forests and decreased it in the 46-year-old forest (p > 0.05); significantly increased the macroaggregates’ δ¹⁵N in the 46-year-old forest (p < 0.05), and decreased the macroaggregates’ δ¹⁵N in the 200-year-old forest (p > 0.05). Considering the distribution of δ¹³C and δ¹⁵N in the aggregates, the effect of nitrogen addition on the dynamic mechanism of soil aggregate carbon and nitrogen fractions varied based on forest age and aggregate size. Correlation analysis further revealed that soil total phosphorus, NH₄⁺-N, NO₃⁻-N, dissolved organic nitrogen, pH, texture, etc., were the primary predictors explaining most of the variation in aggregate fractions and their δ¹³C distribution. In summary, the effect of nitrogen deposition on the carbon and nitrogen stability of soil aggregates in broad-leaved forests depends on forest age. Full article