Zinc (Zn) is a vital micronutrient required for optimal plant growth and soil fertility. Its use in the form of nanoparticles (NPs) has gained significant attention in agricultural applications. Green synthesized Zn-based NPs offer an eco-friendly solution to several conventional problems in agriculture. Several plants, bacteria, fungi and yeast have shown significant potential in fabricating Zn NPs that can provide environmentally friendly solutions in agriculture and the approach is aligned with sustainable agricultural practices, reducing the dependency on harmful agrochemicals. Zn-based NPs act as plant growth promoters, enhance crop yield, promote resilience to abiotic stressors and are efficient crop protection agents. Their role as a smart delivery system, enabling targeted and controlled release of agrochemicals, further signifies their potential use in agriculture. Because agriculture requires repeated applications hence, the toxicological aspects of Zn NPs cannot be ignored. Zn NPs are reported to cause phytotoxicity, including root damage, physiological and biochemical disturbances, and genotoxic effects. Furthermore, exposure to Zn NPs poses risks to soil microbiota, and aquatic and terrestrial organisms potentially impacting the ecosystem. The green synthesis of Zn-based NPs has a promising aspect for advancing sustainable agriculture by reducing agrochemical use and improving crop productivity. Their diverse applications as plant growth promoters, crop protectants and smart delivery systems emphasize their potential. However, the toxicological aspects are essential to ensure the standardization of doses for their safe and effective use. Further research would help address such concerns and help in developing viable and eco-friendly solutions for modern agriculture. (c) 2025 Society of Chemical Industry.

A sustainable use of croplands should utilize beneficial services provided by their resident soil microbiome. To identify potentially adverse environmental effects on soil microbiomes in the future, a better understanding of their natural variability is fundamental. Here, we characterized the abundance and diversity of soil microbial communities over 2 years at two-week intervals on three neighboring fields at an operational farm in Northern Germany. Field soils differed in texture (clay, loam) and tillage (soil conservation vs. conventional). PCRamplicon analyses of soil DNA revealed distinct temporal variations of bacteria, archaea, fungi, and protists (Cercozoa and Endomyxa). Annual differences and seasonal effects on all microbial groups were detected. In addition to soil pH, prokaryotic communities varied with total soil C and N, but fungi with temperature and precipitation. The C/N ratio had contrasting effects on prokaryotic phyla and protistan classes, but all fungal phyla responded positively. Irrespective of the sampling date, prokaryotic and fungal but not protistan community compositions from the three soils were distinct. Compositional turnover rates were higher for fungi and protists than for prokaryotes and, for all, lower in clay. Conventional tillage had the strongest effect on protist diversity. In co-occurrence networks, most nodes were provided by prokaryotes, but highly connected nodes by predatory protists in the first, and by saprotrophic fungi in the second year. The temporal variation established here can provide insights of what is natural and thus below the limits of concern in detecting adverse effects on the soil microbiome.

Snow amounts and duration are susceptible to climate change and may significantly affect plant diversity and biomass in grassland ecosystems. Yet, the combined effects of grassland use (type and intensity) and snow depth on plant diversity and productivity remain poorly understood. We established two complementary field experiments to explore the mechanisms driving the effects of grassland use (type and intensity) and snow manipulation on plant diversity and productivity in the meadow steppe. An experiment on grassland use type and snow manipulation showed that lower snow cover in winter reduced soil moisture in the snowmelt period, significantly increased the abundance of ammonia-oxidizing archaea and ammonia-oxidizing bacteria, and initiated nitrification earlier, resulting in the loss of soil available nitrogen, and then reduced the aboveground biomass of early grasses. An experiment on grassland mowing intensity and snow manipulation showed that moderate mowing intensity can restrain the loss of grass biomass and soil nutrients and maintain grassland sustainability in winters with less snow. Stochasticity has played a more important role in plant community assembly in higher intensity of grassland use. Based on our results, we recommend that optimal defoliation height can restrain the loss of grass biomass and soil nutrients and maintain grassland sustainability in winters with less snow. This study has potential benefits for optimizing sustainable production and maintaining ecosystem function under winter snowfall changes in the future across large regions of arid and semiarid grasslands. (c) 2024 The Society for Range Management. Published by Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.

Soil microbiomes drive many soil processes and maintain the ecological functions of terrestrial ecosystems. Microplastics (MPs, size <5 mm) are pervasive emerging contaminants worldwide. However, how MPs affect soil microbial activity has not been well elucidated. This review article first highlights the effects of MPs on overall soil microbial activities represented by three soil enzymes, i.e., catalase, dehydrogenase, and fluorescein diacetate hydrolase (FDAse), and explores the underlying mechanisms and influencing factors. Abundant evidence confirms that MPs can change soil microbial activities. However, existing results vary greatly from inhibition to promotion and non-significance, depending on polymer type, degradability, dose, size, shape, additive, and aging degree of the target MPs, soil physicochemical and biological properties, and exposure conditions, such as exposure time, temperature, and agricultural practices (e.g., planting, fertilization, soil amendment, and pesticide application). MPs can directly affect microbial activities by acting as carbon sources, releasing additives and pollutants, and shaping microbial communities via plastisphere effects. Smaller MPs (e.g., nanoplastics, 1 to <1000 nm) can also damage microbial cells through penetration. Indirectly, MPs can change soil attributes, fertility, the toxicity of co-existing pollutants, and the performance of soil fauna and plants, thus regulating soil microbiomes and their activities. In conclusion, MPs can regulate soil microbial activities and consequently pose cascading consequences for ecosystem functioning.

The root-knot nematode (RKN) causes significant yield loss in tomatoes. Understanding the interaction of biocontrol agents (BCAs)-nematicides-soil microbiomes and RKNs is essential for enhancing the efficacy of biocontrol agents and nematicides to curb RKN damage to crops. The present study aimed to evaluate the in vitro effectiveness of BACa and nematicide against RKN and to apply the amplicon sequencing to assess the interaction of Bacillus velezensis (VB7) and Trichoderma koningiopsis (TK) against RKNs. Metagenomic analysis revealed the relative abundance of three phyla such as Proteobacteria (42.16%), Firmicutes (19.57%), and Actinobacteria (17.69%) in tomato rhizospheres. Those tomato rhizospheres treated with the combined application of B. velezensis VB7 + T. koningiopsis TK and RKN had a greater frequency of diversity and richness than the control. RKN-infested tomato rhizosphere drenched with bacterial and fungal antagonists had the maximum diversity index of bacterial communities. A strong correlation with a maximum number of interconnection edges in the phyla Proteobacteria, Firmicutes, and Actinobacteria was evident in soils treated with both B. velezensis VB7 and T. koningiopsis TK challenged against RKN in infected soil. The present study determined a much greater diversity of bacterial taxa observed in tomato rhizosphere soils treated with B. velezensis VB7 and T. koningiopsis TK than in untreated soil. It is suggested that the increased diversity and abundance of bacterial communities might be responsible for increased nematicidal properties in tomato plants. Hence, the combined applications of B. velezensis VB7 and T. koningiopsis TK can enhance the nematicidal action to curb RKN infecting tomatoes.

Forest parks in megacities are pivotal in boosting biodiversity, purifying air, and offering essential green areas for community leisure and mental health amidst the hustle and bustle of cities. Yet, these vital oases encounter severe difficulties, including habitat degradation, contamination, and urbanization pressures, jeopardizing their preservation and the crucial ecological advantages they offer. The soil 's characteristics and its microbial inhabitants are fundamental in the cycling of nutrients and the well-being of plants, positioning them as central elements in restoration efforts. Nonetheless, the complex interplay among plant, soil, and microbial relationships during the restoration of forest ecosystems in megacities is still not well comprehended. This study aimed to investigate the interactions between plant-soil-microbial dynamics in different ecological restoration modes and construct assessment systems to evaluate the quality of restoration modes in the forest parks. The study identified a total of 25 distinct types of forests damaged by three main factors (farmland, highway, and quarrying) in Chongqing Taisiya Forest Park, and found that long-term natural restoration significantly increased soil properties in these forests. Additionally, an in-depth microbial sequencing analysis showed that Proteobacteria and Ascomycota were the major bacterial and fungal phyla dominant in the restoration process in the urban forests. Further correlation analysis showed that soil microbial diversity positively correlated with plant diversity, with a stronger correlation observed for bacterial communities compared to fungi. The comprehensive evaluation index results for the different forest types revealed varying degrees of restoration success. Collectively, our findings underscore the importance of forest attributes and soil microbial diversity in forest ecosystem restoration and provide valuable insights for designing effective restoration strategies in similar ecosystems.

Climate change is rapidly transforming Arctic landscapes where increasing soil temperatures speed up permafrost thaw. This exposes large carbon stocks to microbial decomposition, possibly worsening climate change by releasing more greenhouse gases. Understanding how microbes break down soil carbon, especially under the anaerobic conditions of thawing permafrost, is important to determine future changes. Here, we studied the microbial community dynamics and soil carbon decomposition potential in permafrost and active layer soils under anaerobic laboratory conditions that simulated an Arctic summer thaw. The microbial and viral compositions in the samples were analyzed based on metagenomes, metagenome-assembled genomes, and metagenomic viral contigs (mVCs). Following the thawing of permafrost, there was a notable shift in microbial community structure, with fermentative Firmicutes and Bacteroidota taking over from Actinobacteria and Proteobacteria over the 60-day incubation period. The increase in iron and sulfate-reducing microbes had a significant role in limiting methane production from thawed permafrost, underscoring the competition within microbial communities. We explored the growth strategies of microbial communities and found that slow growth was the major strategy in both the active layer and permafrost. Our findings challenge the assumption that fast-growing microbes mainly respond to environmental changes like permafrost thaw. Instead, they indicate a common strategy of slow growth among microbial communities, likely due to the thermodynamic constraints of soil substrates and electron acceptors, and the need for microbes to adjust to post-thaw conditions. The mVCs harbored a wide range of auxiliary metabolic genes that may support cell protection from ice formation in virus-infected cells.IMPORTANCE As the Arctic warms, thawing permafrost unlocks carbon, potentially accelerating climate change by releasing greenhouse gases. Our research delves into the underlying biogeochemical processes likely mediated by the soil microbial community in response to the wet and anaerobic conditions, akin to an Arctic summer thaw. We observed a significant shift in the microbial community post-thaw, with fermentative bacteria like Firmicutes and Bacteroidota taking over and switching to different fermentation pathways. The dominance of iron and sulfate-reducing bacteria likely constrained methane production in the thawing permafrost. Slow-growing microbes outweighed fast-growing ones, even after thaw, upending the expectation that rapid microbial responses to dominate after permafrost thaws. This research highlights the nuanced and complex interactions within Arctic soil microbial communities and underscores the challenges in predicting microbial response to environmental change. As the Arctic warms, thawing permafrost unlocks carbon, potentially accelerating climate change by releasing greenhouse gases. Our research delves into the underlying biogeochemical processes likely mediated by the soil microbial community in response to the wet and anaerobic conditions, akin to an Arctic summer thaw. We observed a significant shift in the microbial community post-thaw, with fermentative bacteria like Firmicutes and Bacteroidota taking over and switching to different fermentation pathways. The dominance of iron and sulfate-reducing bacteria likely constrained methane production in the thawing permafrost. Slow-growing microbes outweighed fast-growing ones, even after thaw, upending the expectation that rapid microbial responses to dominate after permafrost thaws. This research highlights the nuanced and complex interactions within Arctic soil microbial communities and underscores the challenges in predicting microbial response to environmental change.

Bacterial secondary metabolites serve as an important source of molecules for drug discovery. They also play an important function in mediating the interactions of microbial producers with their living environment and surrounding organisms. However, little is known about the genetic novelty, distribution, and community-level impacts of soil bacterial biosynthetic potential on a large geographic scale. Here, we constructed the first catalog of 11,149 biosynthetic gene clusters (BGCs) from agricultural soils across China and unearthed hidden biosynthetic potential for new natural product discovery from the not-yet-cultivated soil bacteria. Notably, we revealed soil pH as the strongest environmental driver of BGC biogeography and predicted that soil acidification and global climate change could damage the biosynthetic potential of the soil microbiome. The co-occurrence network of bacterial genomes revealed two BGC-rich species, i.e., Nocardia niigatensis from Actinobacteriota and PSRF01 from Acidobacteriota, as the module hub and connector, respectively, indicating their keystone positions in the soil microbial communities. We also uncovered a dominant role of BGC-inferred biotic interactions over environmental drivers in structuring the soil microbiome. Overall, this study achieved novel insights into the BGC landscape in agricultural soils of China, substantially expanding our understanding of the diversity and novelty of bacterial secondary metabolism and the potential role of secondary metabolites in microbiota assembly. IMPORTANCE Bacterial secondary metabolites not only serve as the foundation for numerous therapeutics (e.g., antibiotics and anticancer drugs), but they also play critical ecological roles in mediating microbial interactions (e.g., competition and communication). However, our knowledge of bacterial secondary metabolism is limited to only a small fraction of cultured strains, thus restricting our comprehensive understanding of their diversity, novelty, and potential ecological roles in soil ecosystems. Here, we used culture-independent metagenomics to explore biosynthetic potentials in agricultural soils of China. Our analyses revealed a high degree of genetic diversity and novelty within biosynthetic gene clusters in agricultural soil environments, offering valuable insights for biochemists seeking to synthesize novel bioactive products. Furthermore, we uncovered the pivotal role of BGC-rich species in microbial communities and the significant relationship between BGC richness and microbial phylogenetic turnover. This information emphasizes the importance of biosynthetic potential in the assembly of microbial communities.

Clubroot (Plasmodiophora brassicae) is an important soilborne disease that causes severe damage to cruciferous crops in China. This study aims to compare the differences in chemical properties and microbiomes between healthy and clubroot-diseased soils. To reveal the difference, we measured soil chemical properties and microbial communities by sequencing 18S and 16S rRNA amplicons. The available potassium in the diseased soils was higher than in the healthy soils. The fungal diversity in the healthy soils was significantly higher than in the diseased soils. Ascomycota and Proteobacteria were the most dominant fungal phylum and bacteria phylum in all soil samples, respectively. Plant-beneficial microorganisms, such as Chaetomium and Sphingomonas, were more abundant in the healthy soils than in the diseased soils. Co-occurrence network analysis found that the healthy soil networks were more complex and stable than the diseased soils. The link number, network density, and clustering coefficient of the healthy soil networks were higher than those of the diseased soil networks. Our results indicate that the microbial community diversity and network structure of the clubroot-diseased soils were different from those of the healthy soils. This study is of great significance in exploring the biological control strategies of clubroot disease.

BackgroundAntarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with contributions from the bacterial domain restricted to Actinomycetota and Cyanobacteriota. Nevertheless, the ice-free areas of the Antarctic continent and the sub-Antarctic islands are dominated in terms of diversity by bacteria. Our study aims to generate a comprehensive phylogenetic dataset of Antarctic bacteria with wide geographical coverage on the continent and sub-Antarctic islands, to investigate whether bacterial diversity and distribution is reflected in the current ACBRs.ResultsSoil bacterial diversity and community composition did not fully conform with the ACBR classification. Although 19% of the variability was explained by this classification, the largest differences in bacterial community composition were between the broader continental and maritime Antarctic regions, where a degree of structural overlapping within continental and maritime bacterial communities was apparent, not fully reflecting the division into separate ACBRs. Strong divergence in soil bacterial community composition was also apparent between the Antarctic/sub-Antarctic islands and the Antarctic mainland. Bacterial communities were partially shaped by bioclimatic conditions, with 28% of dominant genera showing habitat preferences connected to at least one of the bioclimatic variables included in our analyses. These genera were also reported as indicator taxa for the ACBRs.ConclusionsOverall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities.APsmQ8MphSAgg4BzZyqdNTVideo AbstractConclusionsOverall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities.APsmQ8MphSAgg4BzZyqdNTVideo Abstract