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At least 19 recordsLinked to original sources
PubMed2026

Spiramycin fermentation residue-derived biochar regulates soil nutrient cycling, microbial communities, and antibiotic resistance gene dynamics.

Spiramycin fermentation residues (SFR) are hazardous wastes enriched with residual antibiotics, yet they can serve as potential feedstocks for resource recovery after appropriate treatment. In this study, SFR-derived biochar (SFR-BC) was produced by pyrolysis and applied to agricultural soil to evaluate its effects on soil properties, microbial communities, potential pathogenic bacteria, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). A 60-day soil incubation experiment was conducted with one control and three SFR-BC application rates of 0.5%, 1.0%, and 2.0%. SFR-BC improved soil physicochemical properties, nutrient status, enzyme activities, and microbial alpha diversity. Metagenomic analysis showed that SFR-BC altered the abundance of functional genes associated with carbon and nitrogen cycling, indicating shifts in microbial functional potential. SFR-BC also changed bacterial co-occurrence patterns, with the high-dose treatment showing a more complex and highly connected network structure during incubation. In addition, high-dose SFR-BC reduced several potential pathogenic bacteria, including major plant pathogenic taxa. SFR-BC decreased soil ARG abundance by 9.38%-33.67% and MGE abundance by 6.49%-27.89% relative to the control, showing a dose-dependent reduction in antibiotic resistance-related genetic elements. Network and PLS-PM analyses further indicated that ARG variation was statistically associated with soil physicochemical properties, microbial diversity, potential bacterial hosts, and MGEs. Overall, these results suggest that SFR-BC can improve short-term soil nutrient status and reduce ARGs, MGEs, and several potential pathogenic taxa under controlled incubation conditions, providing useful evidence for the potential valorization of antibiotic fermentation residues through pyrolysis.

Charcoal↗
PubMed2026

Persistent antimicrobial resistance during soil remediation driven by residual heavy metal co-selection.

Remediation of heavy metal-contaminated soil is a global priority, particularly as reclaimed land increasingly intersects with urban development and human exposure. However, the ecological consequences of soil remediation, especially its impact on antimicrobial resistance (AMR) as a global health threat, have remained poorly understood. Here, we combined single-cell Raman-D₂O probing with genome-resolved metagenomics to monitor the dynamics of phenotypic and genotypic resistance to metals and antibiotics during a 120-day remediation of soils with three contamination levels from a lead-zinc smelting site. Although chemical remediation substantially reduced bioavailable metals (by 42%-65%), AMR was not diminished. Instead, both phenotypic activity and gene abundance of metal- and antibiotic-resistant microorganisms increased, resulting in a two- to three-fold increase in AMR-associated health risks. Among 76 metagenome assembled genomes (MAGs) from phenotypic resistance communities, all Cd resistance-associated MAGs harbored multidrug resistance genes, half of which were colocalized with metal resistance determinants, and their prevalence continued to rise with remediation. These findings reveal that although remediation alleviates acute metal toxicity, residual low-concentration bioavailable metals sustain evolutionary selection for resistance, highlighting a disconnect between chemical recovery and biological safety. Moreover, the improved soil nutrient and physiochemical properties of remediated soils further promoted the proliferation of antibiotic-resistant bacteria. This study offers new ecological insights into the unintended consequences of anthropogenic interventions, underscoring the need to integrate biological safety into soil health and safety assessments.

Soil Microbiology↗
PubMed2024

Soil keystone viruses are regulators of ecosystem multifunctionality.

Ecosystem multifunctionality reflects the capacity of ecosystems to simultaneously maintain multiple functions which are essential bases for human sustainable development. Whereas viruses are a major component of the soil microbiome that drive ecosystem functions across biomes, the relationships between soil viral diversity and ecosystem multifunctionality remain under-studied. To address this critical knowledge gap, we employed a combination of amplicon and metagenomic sequencing to assess prokaryotic, fungal and viral diversity, and to link viruses to putative hosts. We described the features of viruses and their potential hosts in 154 soil samples from 29 farmlands and 25 forests distributed across China. Although 4,460 and 5,207 viral populations (vOTUs) were found in the farmlands and forests respectively, the diversity of specific vOTUs rather than overall soil viral diversity was positively correlated with ecosystem multifunctionality in both ecosystem types. Furthermore, the diversity of these keystone vOTUs, despite being 10-100 times lower than prokaryotic or fungal diversity, was a better predictor of ecosystem multifunctionality and more strongly associated with the relative abundances of prokaryotic genes related to soil nutrient cycling. Gemmatimonadota and Actinobacteria dominated the host community of soil keystone viruses in the farmlands and forests respectively, but were either absent or showed a significantly lower relative abundance in that of soil non-keystone viruses. These findings provide novel insights into the regulators of ecosystem multifunctionality and have important implications for the management of ecosystem functioning.

Soil Microbiology↗
PubMed1979

Bioavailability of Cd to Food crops in relation to heavy metal content of sludge-amended soil.

Results of greenhouse and laboratory experiments on factors influencing uptake and accumulation of Cd by economic crops are summarized.Tolerance to Cd is highly crop-specific. For example, 21 different economic crops were grown in pots filled with a calcareous soil treated with increasing amounts of Cd. Yields versus Cd addition rate relations showed yield reductions to occur with Cd sensitive plants (spinach, soybean, curlycress, and lettuce) at addition rates varying from 5 to 15 mug Cd/g soil, whereas tolerant crops (tomato, squash, cabbage, and rice) did not suffer a yield reduction when treated at rates less than 150 mug Cd/g soil. Nutrient solution experiments likewise revealed marked differences in growth of crops. Corn, turnip, beets, bean, and tomato plants grown in solution cultures containing 0.1 mug Cd/ml accumulated different amounts of Cd in leaf tissue depending upon crop species; leaf Cd concentrations ranged from a low of 9 mug Cd/g leaf for beans to 200 mug Cd/g leaf for beets. Large differences also occur with regard to distribution of Cd within the plant. Fruit and seed tissue contain less Cd than leaves. Experiments comparing the toxicity of Cd to Cu, Ni, and Zn in an acid soil +/- lime showed Cd to be the most phytotoxic. While interactive effects occur with regard to metal uptake and accumulation by plants, Cd uptake is essentially dependent upon the Cd concentration of the soil. Studies of chemical speciation of Cd in relation to Cd availability indicate that the free Cd(2+) concentration correlates better with Cd uptake than Cd total of the soil solution.

Agriculture↗
PubMed2025

Balancing nutrient remobilization and photosynthesis: proteomic insights into the dual role of lupin cotyledons after germination.

Efficient nutrient mobilization from seed storage tissues is essential for seedling establishment, particularly in legumes such as Lupinus albus (white lupin), which thrive in nutrient-poor soils. This study investigates the role of cotyledons in nitrogen (N) and mineral remobilization after germination during their transition from storage organs to photosynthetically active tissues, including the metabolic challenges posed by the coexistence of these two functions in epigeal germination. We cultivated white lupin seedlings under nitrogen-deficient conditions, analyzing cotyledon composition and function over 28 days. Our results indicate that 60% of cotyledon-stored proteins are degraded within the first 8 days, with free amino acids transiently accumulating before being redistributed to support growth. The progressive depletion of cotyledon reserves was accompanied by structural and metabolic changes, including an increase in photosynthetic proteins. However, cotyledon photosynthetic capacity remained lower than that of true leaves, suggesting a transient role in energy metabolism. The loss of cotyledons before day 12 significantly impaired seedling development, emphasizing their critical contribution to nitrogen, phosphate, and micronutrient supply during early growth. Comparative proteomic analysis revealed dynamic shifts in nutrient transport, amino acid metabolism, and stress response pathways following cotyledon removal. These findings underscore the significance of cotyledon nutrient remobilization in legume adaptation to low-fertility soils and highlight potential targets for breeding strategies aimed at improving nutrient use efficiency. By optimizing cotyledon nutrient composition and function, future breeding efforts could enhance seedling vigor, reduce fertilizer dependency, and improve the nutritional value of lupin-based foods.

Lupinus↗
PubMed2026

Multi-omics reveal microbial functional traits and antifungal metabolites associated with lower Pseudogymnoascus destructans loads in bat cave soils.

White-nose syndrome, caused by Pseudogymnoascus destructans (Pd), is a major fungal disease threatening hibernating bats. Cave soils can serve as environmental reservoirs for Pd, yet the microbial and biochemical mechanisms underlying naturally low Pd burdens in some cave environments remain poorly understood. Here, we integrated soil microbiome profiling, metagenomics, metabolomics, multi-omics network analysis, and in vitro validation to investigate the ecological and functional basis of differential Pd loads in hibernating bat caves in Northeast China. The three caves shared cold, humid, and weakly acidic microenvironments, but differed significantly in electrical conductivity, soil water content, nutrient availability, and extracellular enzyme activities. Soil microbial communities showed significant inter-cave variation in composition, diversity, and niche breadth, with stochastic processes contributing substantially to community assembly. Environmental variables, particularly pH and Pd load, were important predictors of microbial community structure. Functional analyses revealed that the low-Pd Gezi Cave was enriched in genes associated with organic carbon degradation, nitrogen input and retention, and secondary metabolism. Metabolomic profiling further identified cave-specific metabolite signatures, among which Biochanin A, 4-Hydroxybenzaldehyde, Vanillin, and Arachidonic acid were negatively correlated with Pd loads. Integrated pathway and network analyses showed that differential genes and metabolites jointly mapped to secondary metabolite biosynthesis, aminobenzoate degradation, and flavonoid degradation pathways, forming a microbe-metabolite-functional gene coupling network involving key taxa such as Rhodococcus, Pseudorhodoplanes, and Rhodoplanes. In vitro assays confirmed that 4-Hydroxybenzaldehyde, Coumarin, and Vanillin inhibited Pd growth. Structural equation modelling further indicated that environmental heterogeneity was associated with variation in Pd loads through microbial functional attributes and metabolite profiles. These findings suggest that naturally low-Pd cave soils are associated with coordinated environmental filtering, microbial functional specialization, and antifungal metabolite production, providing mechanistic insight into microbial and biochemical constraints on Pd persistence in cave reservoirs.

Animals↗
PubMed2026

Soil Acidification Enriches Antibiotic Resistome.

Soil acidification represents a critical global change issue. Its impacts on antibiotic resistance genes (ARGs), however, remain poorly understood. Here we first analyzed a published global dataset comprising 1012 sampling sites and found a significant negative correlation between soil pH and the total richness and relative abundance of ARGs. To validate the observed pattern, we subjected three soils (with initial pH 7.8-7.9) each to 4 acidification levels (pH 7, 6, 5, and 4) for 30 days and subsequent recovery for another 30 days in microcosms. Shotgun metagenomic sequencing revealed that acidification (pH 6, 5, and 4) significantly increased the total richness and relative abundance of ARGs, as well as the relative abundances of 175 ARG subtypes, across all three soils. These 175 acidification-enriched ARGs together accounted for more than 70% of all the ARGs under severely acidified conditions (pH 5 and 4). Moreover, 93% of the bacteria carrying acidification-enriched ARGs also carried various virulence factor genes homologs associated with pathogenicity in reference databases, resulting in increased risk score. The total relative abundance of the acidification-enriched ARGs was primarily associated with changes in bacterial community traits (community composition, acidification-enriched metabolic functions, and genome size), followed by the increase in availability of toxic metals. When soil recovered from severe acidification (pH 5 and 4), the total relative abundance of the acidification-enriched ARGs significantly declined, demonstrating that the effect of soil acidification is partially reversible. This study reveals an underrecognized risk of ARGs caused by soil acidification, highlighting that the prevention and mitigation of soil acidification are crucial for combating antibiotic resistance.

Hydrogen-Ion Concentration↗
PubMed2026

Long-term saline-alkaline selection rewires the growth-survival trade-off in Priestia megaterium.

Saline-alkaline soils impose persistent osmotic, ionic, pH, and nutrient stress on soil microorganisms, but the evolutionary routes by which beneficial bacteria adapt to such conditions remain poorly resolved. We performed adaptive laboratory evolution to examine the adaption of the plant growth-promoting rhizobacterium Priestia megaterium HA22 to long-term oligotrophic saline-alkaline selection. After 175 serial transfers, the evolved lineage proliferated stably at 40 g L-1 Na2SO4 at pH 10.0, whereas the wild-type strain failed to proliferate. Genome resequencing and allelic replacement revealed a 5-bp insertion in spo0A, the master sporulation regulator, as a major adaptive mutation. This mutation abolished sporulation; shortened the lag phase; and enhanced vegetative growth, nutrient uptake, and expression of tricarboxylic acid cycle and nitrogen metabolism gene under saline-alkaline stress. According to untargeted metabolomics, adaptation was accompanied by increased amino acid metabolism and aminoacyl-tRNA biosynthesis, with proline, isoleucine and pantothenic acid functionally promoting growth. A point mutation in ugpB enhanced glycerol-3-phosphate uptake, increased peptidoglycan and wall teichoic acid levels, and partially rescued the survival cost of the spo0A mutation. In greenhouse assays under combined saline-alkaline stress, the evolved strain increased soybean shoot dry weight and root dry weight by 56.08% and 27.02%, respectively. These results indicate that prolonged, predictable saline-alkaline selection can favor active growth rather than dormancy when compensatory cell envelope reinforcement buffers survival costs.

Adaptive laboratory evolution↗
PubMed1979

Laboratory simulations of the Viking labeled release experiment: kinetics following second nutrient injection and the nature of the gaseous end product.

Injection of 14C-labeled nutrient onto Mars soil produced an evolution of 14C gas in the Viking Labeled Release (LR) experiment. However, a second injection of nutrient seven days later was followed by an abrupt diminution of the amount of radioactive gas in the test cell. Simulation experiments performed in the LR Test Standards Module (TSM) have yielded a plausible explanation for this diminution. Radioactive carbon gases were injected into the TSM test cell in the presence and absence of two Mars analog soils. After equilibration, water was injected and its effect observed. The results indicate that the flight data following second nutrient injection can be explained on a physico-chemical basis involving a carbon dioxide/water/soil equilibrium in the test cell. The results also suggest that the gaseous end product of the Labeled Release reaction on Mars is more likely carbon dioxide than carbon monoxide.

Carbon Radioisotopes↗
PubMed1978

Interaction of atrazine with soil microorganisms: population changes and accumulation.

A loam soil treated with atrazine at rates of 10, 30, and 100 microgram/g soil resulted in increased populations of actinomycetes, bacteria, and fungi over those in non-treated soil. The increases were in proportion to the amount of atrazine and persisted for at least 2 months. Living actinomycete amd fungal mycelia were incubated for 48 h in distilled water, nutrient broth, or soil containing 5 microgram/ml (g) of the herbicide. Actinomycete and fungal mycelia accumulated atrazine from water to concentrations up to 87-fold and 132-fold, respectively, over that in the ambient medium. The maximum accumulation from soil by actinomycete mycelia was 26-fold and by fungal mycelia 13-fold. Fungi accumulated little or no atrazine from a nutrient medium whereas actinomycetes accumulated up to 13-fold. Dead mycelia usually did not accumulate atrazine in excess of the ambient concentration. Mycelium of Sclerotium rolfsii growing in a nutrient medium containing 20 microgram atrazine/ml accumulated 157 microgram/g wet weight after 8 days. Sclerotia subsequently produced after transfer of similar mats to soil contained 550 microgram/g wet weight.

Actinomycetales↗
PubMed2025

Native edaphoclimatic regions shape soil communities of crop wild progenitors.

Unveiling the soil biological communities ecologically associated with crop wild progenitors (CWPs) in their habitats of origin is essential for advancing productive and sustainable agriculture. A field survey was conducted to investigate the edaphoclimatic conditions and soil bacterial, fungal, protist, and invertebrate communities of 125 populations of direct progenitors of major crops for world agriculture. The wild populations clustered into four ecoregions shaped by two edaphoclimatic dimensions: one summarizing variations in soil sand contents and nutrients concentrations, and the other featuring changes in aridity, soil pH, and carbon storage potential. We identified a common soil core community across CWPs that varied significantly along deserts to tropical seasonal forests and savannas. The assembly of the soil core community was driven by varying environmental preferences amongst soil biodiversity kingdoms, reflecting potential shifts in their functional profiles. The tropical ecoregion exhibited higher proportion of acidophilic bacteria, fungal, and protist parasites, whilst desert ecosystems harboured greater abundances of saprophytic fungi and heterotrophic protists. Moreover, CWPs displayed unique microhabitats that incorporate variability into the soil community assembly. Our work reveals the biogeography of soil communities associated with CWPs, the first step towards the development of microbial rewilding initiatives.

centres of origin↗
PubMed1978

A method for the detection and analysis of growth patterns of microorganisms in soil.

A fluorescence-staining technique using the magnesium salt of 8-anilino-1-naphthalene sulfonic acid is described and used to follow the changes in the distribution patterns of microorganisms in soils. A statistical procedure was used to determine the occurrence of significant differences in clumping of bacteria (i.e., production of colonies) in different regions of artificial soil-aggregate systems treated with nutrient solutions and also with a herbicide, Linuron. The response of soil microorganisms to glucose amendment was most marked in the aerobic, outer zone of aggregates. Linuron inhibited colony formation in aggregates treated with the herbicide. The method allows continued observations to be made on the same soil sample at intervals during incubation and os can be used to determine growth rates, inhibitory effects of chemicals, distribution patterns in soils, effects of added nutrients, and other effects where growth in situ is important.

Anilino Naphthalenesulfonates↗
PubMed2026

Dynamics of soil fungal communities restored with biochar from a quarry site.

Quarrying activities have intensified due to population expansion, leading to landscape degradation and ecological destruction. Quarry restoration is usually mandatory in Hong Kong, China. Although biochar is used for sustainable soil amendment, its effectiveness in restoring quarry soil with poor properties has rarely been investigated. A 24-month field study was conducted to evaluate the ecological feasibility of restoring a quarry site by using native species (that is, Castanopsis fissa and Cyclobalanopsis edithiae) and biochar amendment. The results revealed that after 24 months, the application of biochar increased the organic carbon, phosphorus and potassium of the vegetated soil by at least 120 %, 31 % and 12 %, respectively, due to higher cation exchange capacity and better plant growth. The relative abundance of Ascomycota and Basidiomycota increased by 24 % and 47 % with biochar application when C. fissa was planted, which was likely associated with the improved nutrient cycling and soil fertility. Even though adding biochar to bare soil was found to increase the complexity of fungal co-occurrence networks, biochar application only increased fungal diversity in vegetated quarry soil but usually reduced its fungal richness. Moreover, fungal co-occurrence networks in vegetated soil became less complex, suggesting that biochar potentially helped plants to assemble specific, beneficial fungal communities. This effect is most pronounced in the soil planted with C. edithiae, where the structure of fungal communities after 24 months was significantly different from that at other restoration times. This study identifies key fungal phyla enhanced by biochar in quarry soil and provides an effective strategy for facilitating the restoration and management of degraded lands, especially quarry sites.

Charcoal↗
PubMed2026

Artificial intelligence-driven advancements in agricultural biotechnology.

The need for faster and more informative data processing for better decision-making is driving the adoption of artificial intelligence (AI) in the agricultural sector. Thanks to recent advancements in computer science and the increase in computational powers of modern computers, AI is not only augmenting traditional solutions, but also helping in developing novel solutions to existing challenging matters. AI-driven models have an exceptional ability to identify patterns and combine a diverse collection of data together and make inference. The increasing pressure on farmlands posed by the growing global population and climate change is lessening growth, yield, and productivity ultimately posing risk to food security worldwide. Incorporation of AI in agriculture has the potential to drive farming efficiency to new heights. This comprehensive review critically evaluates the evolution of AI in agricultural biotechnology from a theoretical concept to a global phenomenon. A comprehensive literature search was performed using major scientific databases, including PubMed, Web of Science, Embase, Scopus, Lens and the Cochrane Library. In this review, we empirically demonstrate the fields advancement toward more capable AI systems and discuss the current applications of AI across crop improvement and precision agriculture such as crop improvement and genetic engineering, genomic selection and plant breeding, pest and disease detection, precision agriculture and smart farming, soil health and nutrient management, climate resilient crop development, livestock biotechnology, challenges and ethical considerations in AI based agricultural biotechnology. Furthermore, this review addresses the exponential growth of commercial intellectual property in the field and contrast it with academic publication outputs. Finally, we critically assess the ethical challenges impeding equitable adoption of AI including data sovereignty and digital divide, while projecting future frontiers involving quantum computing. This review will help build sustainable agricultural systems capable of adapting to climate change, contribute to the development of climate-resilient and high-yielding crops, and address global food security challenges.

Agriculture↗
PubMed2026

Extreme climatic events drive consistent and predictable shifts in soil antibiotic resistance genes.

Antimicrobial resistance (AMR) is a growing One Health challenge, and as climate warming intensifies extreme events, it remains unclear how these disturbances affect soil antibiotic resistance genes (ARGs). Here we analyzed the data from a controlled experiment using soils from 30 grassland sites across ten European countries, which simulated drought, flooding, freeze-thaw, and heatwaves to explore ARG dynamics. Overall, ARGs exhibited relatively small but highly consistent shifts across treatments. Heatwaves caused the strongest reductions in ARG abundance and in their linkages with mobile genetic elements (MGEs), a pattern that may reflect a hypothesized metabolic-genetic trade-off, in which microbial investment may shift from core metabolism toward stress signaling and structural maintenance. ARG dynamics during and after disturbance were governed by distinct soil physicochemical properties, with temperature and nutrient status determining acute responses, whereas soil moisture and seasonal variability in temperature and precipitation shaped longer-term legacy effects. Cross-validated random-forest models showed positive predictive performance for Bray-Curtis-based compositional responses within the environmental range represented by the 30 grassland sites. Our findings enhance the understanding of how soil ARGs respond to extreme climatic events and provide a step toward predicting extreme-event impacts on soil resistomes with relevance to One Health.

Soil Microbiology↗
PubMed1975

Physiological differences among isolates of Phytophthora cinnamomi.

Significant differences in amylase, beta-glucosidase, and phosphatase activities were observed among four Phytophthora cinnamomi isolates grown in nutrient-amended sterilized soil for 20 days. Amylase pH optima for the four isolates were within a relatively narrow range; at pH 5.5 each isolate was within 90% of its peak activity. Isolates SB-216-1, 1-281, and C-39 each exhibited maximal beta-glucosidase activity at pH 5.0 and maximal phosphatase activity at pH 5.0-5.5. Maximal activity for these two enzymes of isolate A-7725 occurred at pH 3.5. In timed experiments, isolates 1-281 and A-7725 exhibited greater amylase activities than did the other two isolates. For beta-glucosidase, greatest activity was observed for SB-216-1; ACTivity of 1-281 was intermediate and least activity was observed for isolates A-7725 and C-39. Isolates SB-216-1 and 1-281 exhibited greatest phosphatase activities; isolate C-39 was intermediate in activity, and A-7725 was least active. Results indicate that significant differences exist among the isolates tested and that these differences can be quantitatively measured by the methods described.

Amylases↗
PubMed1979

Effect of environmental parameters on the biodegradation of oil sludge.

A laboratory study was conducted with the aim of evaluating and optimizing the environmental parameters of "landfarming", i.e., the disposal by biodegradation in soil of oily sludges generated in the refining of crude oil and related operations. Oil sludge biodegradation was monitored by CO2 evolution and by periodic analysis of residual hydrocarbons. The parameters studied were soil moisture, pH, mineral nutrients, micronutrients, organic supplements, treatment rate, teratment frequency, and incubation temperature. Oil sludge biodegradation was optimal at a soil water-holding capacity of 30 to 90%, a pH of 7.5 to 7.8, C:N and C:P ratios of 60:1 and 800:1, respectively, and a temperature of 20 degrees C or above. Addition of micronutrients and organic supplements was not beneficial; sewage sludge interfered with hydrocarbon biodegradation. Breakdown of the saturated hydrocarbon (alkane and cycloalkane) fraction was the highest at low application rates, but higher application rates favored the biodegradation of the aromatic and asphaltic fractions. An application rate of 5% (wt/wt) oil sludge hydrocarbon to the soil (100,000 liters/hectare) achieved a good compromise between high biodegradation rates and efficient land use and resulted in the best overall biodegradation rate of all hydrocarbon classes. Frequent small applications resulted in higher biodegradation than single large applications. Two 100,000-liter/hectare (255 barrels per acre) or four 50,000-liter/hectare oil sludge hydrocarbon applications per growing season seem appropriate for most temperate zone disposal sites.

Bacteria↗