Soil Community Research Articles

Effective Microbial Strategies to Remediate Contaminated Agricultural Soils and Conserve Functions

The growing global emphasis on sustainable agriculture has brought increased attention to the health and productivity of soils, especially through the lens of soil microbiology. Microbial communities in soil are essential for nutrient cycling, organic matter decomposition, and maintaining overall soil health. However, agricultural practices, including synthetic fertilizers and intensive farming, have led to short time impacts in these microbial ecosystems, potentially threatening soil fertility and environmental quality. Agricultural expansion and food production generate waste and chemical inputs, such as heavy metals, pesticides, and herbicides, leading to significant environmental contamination. This scenario requires the implementation of remediation strategies that are both sustainable and energy efficient. In this context, microbiological processes present a much promising approach to mitigating the environmental impacts of soil pollution. Techniques such as bioremediation, which harness the natural metabolic capabilities of soil microorganisms, and bioaugmentation, which involves the introduction of specific microbial strains to increase degradation processes, are being explored. These approaches are vital for restoring soil health, contributing to environmental conservation and soil biodiversity, improving nutrient cycling, and promoting long-term agricultural productivity.

Short-term organic fertilizer substitution increases sorghum yield by improving soil physicochemical characteristics and regulating microbial community structure

IntroductionChemical fertilizer reduction combined with organic fertilizer (organic fertilizer substitution) has a positive impact on crop productivity and sustainable development. However, the effects of short-term organic fertilizer substitution on microbial community structure and functions of sorghum rhizosphere soil and on sorghum yield remain unclear. Herein, this study investigated the short-term effects of organic fertilizer substitution on sorghum soil physicochemical properties, microbial community structure and enzyme activities using Metagenomic sequencing technology.MethodsThe fertilization treatment included no fertilization (CK), pure chemical fertilizer N (CF), substitution of 25% chemical fertilizer N with organic N (NF25), substitution of 50% chemical fertilizer N with organic N (NF50), substitution of 75% chemical fertilizer N with organic N (NF75), and pure organic fertilizer N (NF100); soil samples were collected and analyzed in the flowering period of sorghum.Results and DiscussionThe results showed that the suitable organic fertilizer substitution rate of sorghum field was 50%, and its yield was the highest among all treatments (9789.9 kg/hm2). Compared with the CF treatment, a medium ratio (50%) of organic fertilizer substitution significantly reduced soil alkalization (by 3.05%), improved soil nutrients, enhanced soil enzyme activities, and increased sorghum yield (P < 0.05). After organic fertilizer substitution treatment, higher protein, fat, and total starch levels accumulated in sorghum grains, and the tannin content of grains decreased. The effect of organic fertilizer substitution on bacterial diversity was greater than that on fungal diversity. Among the dominant bacterial phyla, the medium ratio of organic substitution treatment significantly increased the relative abundances of Proteobacteria (by 3.57%) and Actinomycetes (by 14.94%), and decreased the relative abundances of Acidobacteria (by 5.18%) and Planctomycetes (by 7.76%) compared with no fertilization, while the dominant fungal phyla did not respond significantly to the addition of organic fertilizer. Organic fertilizer substitution also improved soil microbial metabolic pathways, biosynthesis of secondary metabolites, and carbon metabolism. The biomarkers enriched in inorganic fertilizer treatment and organic fertilizer substitution treatments had similar relevant environmental elements but reversed correlation trends. Moreover, soil Alkali-hydrolyzable nitrogen and L-leucine aminopeptidase were important environmental factors influencing the structure of bacterial and fungal communities in sorghum soils, respectively. Soil nutrient levels and microbial communities together explained the variation in annual sorghum yield. The results of this study provide evidence that short-term organic fertilizer substitution increases sorghum yield by improving soil properties and regulating microbial community structure.

Investigating the effects of various irrigation methods on bacterial communities in paddy soil

Different irrigation methods can impact the micro-ecological environment of paddy soil, affecting crop growth. This study focuses on County A, a key grain production area on China’s East Coast, where 20 plots each of intermittent and flood irrigation were selected and labeled as Group I and Group F, respectively. Soil's basic physicochemical properties and heavy metal content were measured in the laboratory, and high-throughput sequencing was used to analyze soil bacterial communities. The study evaluated the impact mechanisms of different irrigation methods on these bacterial communities. Results indicate: (1) Intermittent irrigation significantly increased bacterial richness, evenness, and diversity, enhancing microbial community diversity and stability. (2) Intermittent irrigation notably raised the abundance of 9 bacterial genera (e.g., Nitrospira, H16) while reducing the abundance of 7 genera (e.g., Geobacter, Sphingomonas). (3) The soil environment in Group I was stable, with bacterial communities influenced by SMC, pH, and Cu; Group F was affected by multiple environmental factors. Intermittent irrigation provides a stable environment that supports bacterial diversity and abundance, contributing to a richer community structure. (4) Intermittent irrigation optimizes moisture, significantly enhancing bacterial functions such as energy production, cell wall biosynthesis, repair, and signal transduction. These findings suggest that intermittent irrigation improves bacterial community stability and diversity, which is crucial for enhancing the overall quality of paddy fields.

The Impact of Grafting with Different Rootstocks on Eggplant (Solanum melongena L.) Growth and Its Rhizosphere Soil Microecology

This study investigated the effects of grafting on eggplant growth, yield, and disease resistance, with a focus on microbial dynamics in the rhizosphere. Eggplant scions were grafted onto rootstocks of wild eggplant and tomato, with self-rooted eggplants serving as controls. Greenhouse experiments were conducted over an eight-month growing period, using standard field practices such as film mulching and integrated water–fertilizer management. High-throughput sequencing was used to analyze the biological properties and microbial community of the rhizosphere soil. Results showed that plants grafted onto ‘Huimei Zhenba’ and ‘Torvum’ rootstocks yielded up to 36.89% more than self-rooted controls, achieving yields of 4619.59 kg and 4399.73 kg per 667 m², respectively. The disease incidence of bacterial wilt was reduced to as low as 3.33% in the ‘Huimei Zhenba’ treatment, compared to 55.56% in non-grafted controls. Additionally, grafted plants exhibited increased stem diameter and chlorophyll content, with the TL/HM combination reaching 54.23 ± 3.17 SPAD units. The enhanced microbial biomass of carbon, nitrogen, and phosphorus, particularly in the TL/HM treatment (377.59 mg/kg, 28.31 mg/kg, and 36.30 mg/kg, respectively), supports a more nutrient-rich rhizosphere environment. Moreover, soil enzyme activities, such as β-glucosidase and phosphatase, were significantly higher in grafted plants, enhancing nutrient cycling and potentially increasing resistance to pathogens. Overall, grafted eggplants demonstrated enhanced soil microbial biomass, enzyme activity, and a more diverse microbial community, which are critical factors contributing to the improved yield and disease resistance observed in grafted crops.

Rhizosphere bacterial community is mainly determined by soil environmental factors, but the active bacterial diversity is mainly shaped by plant selection.

The assembly of the rhizosphere community, even the diazotroph community, is mainly shaped by soil environmental factors (including soil climate and physiochemical characteristics) and plant selection. To better understand the driving forces on the active overall and nitrogen-fixing bacterial community compositions, we characterized the communities of tobacco rhizosphere soil collected from three sampling sites with a large geographic scale (> 600km). The results indicate that the diversity and community composition of the overall bacterial and diazotroph communities are obviously differed according to the sampling sites. Still, no significant difference is found between the communities in rootzone and rhizosphere samples. Climate variables including mean annual precipitation (MAP) and mean annual temperature (MAT), soil physiochemical characteristics including available nitrogen (AN), available potassium (AK) and pH are main factors that affect the bacterial and diazotroph community structures in the three sampling sites. Furthermore, MAP and MAT, AN and available phosphorus (AP), total nitrogen (TN) and organic carbon (OC), AK and electrical conductivity (EC) showed similar effects, but pH showed independent effect on the composition of the overall bacteria and diazotroph communities. However, the alpha diversity indices of active overall and nitrogen-fixing bacteria in the rhizosphere are obviously higher than in the rootzone samples, and no significant differences are observed among different sampling sites. Proteobacteria is the predominant active phylum of all samples for overall and nitrogen-fixing bacteria. Escherichia-Shigella, Achromobacter, Streptomyces and Sphingomonas are the dominant active bacterial genera, and Bradyrhizobium, Skermanella and Extensimonas are dominant active nitrogen-fixing bacteria genera in rhizosphere. Furthermore, the high active abundance of Escherichia-Shigella but low abundance of Ralstonia in all three sampling sites indicate high root-knot nematode infection and low wilt disease endemic risk. These results indicate that soil environmental factors contribute more to the tobacco rhizosphere bacterial community assemblage, but the rhizosphere contributes more to the diversity of active overall bacteria and nitrogen-fixing bacteria in the community. Our study provides novel knowledge for the assemble of rhizosphere bacterial and active bacteria communities across a large geographical scale.

Unravelling the Molecular Dialogue of Beneficial Microbe-Plant Interactions.

Plants are an intrinsic part of the soil community, which is comprised of a diverse range of organisms that interact in the rhizosphere through continuous molecular communications. The molecular dialogue within the plant microbiome involves a complex repertoire of primary and secondary metabolites that interact within different liquid matrices and biofilms. Communication functions are likely to involve membrane-less organelles formed by liquid-liquid phase separation of proteins and natural deep eutectic solvents that play a role as alternative media to water. We discuss the chemistry of inter-organism communication and signalling within the biosphere that allows plants to discriminate between harmful, benign and beneficial microorganisms. We summarize current information concerning the chemical repertoire that underpins plant-microbe communication and host-range specificity. We highlight how the regulated production, perception and processing of reactive oxygen species (ROS) is used in the communication between plants and microbes and within the communities that shape the soil microbiome.

Effects of Polycyclic Aromatic Hydrocarbons on Soil Bacterial and Fungal Communities in Soils

Soil organic pollution (such as heavy metals, PAHs, etc.) has caused serious environmental problems, which have resulted in unexpected effects on contaminated soil ecosystems. However, knowledge of the interactions between environmental PAHs and bacterial and fungal communities is still limited. In this study, soil samples from different PAH-contaminated areas including non-contaminated areas (NC), low-contaminated areas (LC), and high-contaminated areas (HC) were selected. Results of toxic equivalent quantity (TEQ) indicated that Benzo[a]pyrene (BaP) and Dibenzo[a,h]anthracene (DBahA) constituted the main TEQs of ∑16PAHs. Incremental lifetime cancer risk (ILCR) assessment revealed that the main pathway of exposure to soil PAHs was dermal contact in adults and children. Furthermore, adults faced a higher total cancer risk (including dermal contact, ingestion, and inhalation) from soil PAHs than children. The microbial community composition analysis demonstrated that soil PAHs could decrease the diversity of bacterial and fungal communities. The relative abundance of Acidobacteriota, Gemmatimonadota, Fimicutes, Bacteroidota, Ascomycota, and Basidiomycota exhibited varying degrees of changes under different concentrations of PAHs. Benzo[a]anthracene (BaA) and Chrysene (Chr) drove the bacterial community composition, while BaP and DBahA drove the fungal community compositions. Co-occurrence network analysis revealed the high contamination levels of PAHs that could change the relationships among different microorganisms and reduce the complexity and stability of fungal and bacterial networks. Overall, these findings provide comprehensive insight into the responses of bacterial and fungal communities to PAHs.

Mycorrhizal and endophytic fungi structure forest below-ground symbiosis through contrasting but interdependent assembly processes

BackgroundInteractions between plants and diverse root-associated fungi are essential drivers of forest ecosystem dynamics. The symbiosis is potentially dependent on multiple ecological factors/processes such as host/symbiont specificity, background soil microbiome, inter-root dispersal of symbionts, and fungus–fungus interactions within roots. Nonetheless, it has remained a major challenge to reveal the mechanisms by which those multiple factors/processes determine the assembly of root-associated fungal communities. Based on the framework of joint species distribution modeling, we examined 1,615 root-tips samples collected in a cool-temperate forest to reveal how root-associated fungal community structure was collectively formed through filtering by host plants, associations with background soil fungi, spatial autocorrelation, and symbiont–symbiont interactions. In addition, to detect fungi that drive the assembly of the entire root-associated fungal community, we inferred networks of direct fungus–fungus associations by a statistical modeling that could account for implicit environmental effects.ResultsThe fine-scale community structure of root-associated fungi were best explained by the statistical model including the four ecological factors/processes. Meanwhile, among partial models, those including background soil fungal community structure and within-root fungus–fungus interactions showed the highest performance. When fine-root distributions were examined, ectomycorrhizal fungi tended to show stronger associations with background soil community structure and spatially autocorrelated patterns than other fungal guilds. In contrast, the distributions of root-endophytic fungi were inferred to depend greatly on fungus–fungus interactions. An additional statistical analysis further suggested that some endophytic fungi, such as Phialocephala and Leptodontidium, were placed at the core positions within the web of direct associations with other root-associated fungi.ConclusionBy applying emerging statistical frameworks to intensive datasets of root-associated fungal communities, we demonstrated background soil fungal community structure and fungus–fungus associations within roots, as well as filtering by host plants and spatial autocorrelation in ecological processes, could collectively drive the assembly of root-associated fungi. We also found that basic assembly rules could differ between mycorrhizal and endophytic fungi, both of which were major components of forest ecosystems. Consequently, knowledge of how multiple ecological factors/processes differentially drive the assembly of multiple fungal guilds is indispensable for comprehensively understanding the mechanisms by which terrestrial ecosystem dynamics are organized by plant–fungal symbiosis.

Salinity drives niche differentiation of soil bacteria and archaea in Hetao Plain, China

Soil salinization is a critical environmental issue that limits plant productivity and disrupts ecosystem functions. As important indicators of soil environment, soil microbes play essential roles in driving nutrient cycling and sustaining ecosystem services. Therefore, understanding how microbial communities and their functional potentials respond to varying levels of soil salinization across different land use types is crucial for the restoration and management of salt-affected ecosystems. In this study, we randomly selected 63 sites across the Hetao Plain, covering an area of ∼2500 km2. Our results showed that both salinity- and fertility-related soil parameters were significantly correlated with bacterial and archaeal diversities, with soil salinity emerging as the stronger predictor of prokaryotic diversity. Intriguingly, bacterial and archaeal communities were tightly interlinked but displayed opposite trends in response to environmental factors, indicating a clear microbial niche differentiation driven by soil salinity. Moreover, the generalist functions of bacteria and archaea (e.g., chemoheterotrophy) exhibited contrasting responses to environmental parameters, while their specialist functions (e.g., nitrification) responded consistently. These findings highlight the pivotal role of soil salinity in shaping the niche differentiation of bacterial and archaeal communities in saline soils, providing insights to guide salinity-centered restoration strategies for effective marginal land management.

Planting density effect on poplar growth traits and soil nutrient availability, and response of microbial community, assembly and function

BackgroundThe interaction between soil characteristics and microbial communities is crucial for poplar growth under different planting densities. Yet, little is understood about their relationships and how they respond to primary environmental drivers across varying planting densities.ResultsIn this study, we investigated poplar growth metrics, soil characteristics, and community assembly of soil bacterial and fungal communities in four poplar genotypes (M1316, BT17, S86, and B331) planted at low, medium, and high densities. Our findings reveal that planting density significantly influenced poplar growth, soil nutrients, and microbial communities (P < 0.05). Lower and medium planting densities supported superior poplar growth, higher soil nutrient levels, increased microbial diversity, and more stable microbial co-occurrence networks. The assembly of bacterial communities in plantation soils was predominantly deterministic (βNTI < -2), while fungal communities showed more stochastic assembly patterns (-2 < βNTI < 2). Soil available phosphorus (AP) and potassium (AK) emerged as pivotal factors shaping microbial communities and influencing bacterial and fungal community assembly. Elevated AP levels promoted the recruitment of beneficial bacteria such as Bacillus and Streptomyces, known for their phosphate-solubilizing abilities. This facilitated positive feedback regulation of soil AP, forming beneficial loops in soils with lower and medium planting densities.ConclusionsOur study underscores the critical role of planting density in shaping soil microbial communities and their interaction with poplar growth. This research carries significant implications for enhancing forest management practices by integrating microbiological factors to bolster forest resilience and productivity.

Pecan-medicinal crops intercropping improved soil fertility and promoted interactions between soil microorganisms and metabolites

BackgroundPecan [Carya illinoinensis (Wangenh.) Koch] is a widely cultivated dried fruit and woody oil tree with high economic value. Continuous sole planting of pecan caused some land to lie idle and deterioration of soil conditions. Tree and medicinal crops intercropping represents an environmental-friendly and economically feasible solution to these issues. Thus, we aimed to explore the underlying mechanism by which intercropping improved soil condition by regulating the interactions of the soil microbiome and metabolome. In this study, pecans were intercropped with medicinal crops caper spurge and honeysuckle on a tree farm in China. A combined analysis of soil microbiomes and metabolomes was performed to discover the effects of intercropping on bulk and rhizosphere soils.ResultsThe results showed that intercropping improved the edaphic properties of bulk soil and promoted the growth of pecan and caper spurge. Intercropping also significantly altered the structures of both bacterial and fungal communities in bulk soil, stabilised the enrichment of nitrogen-cyclic bacteria, for instance, Bacillus, and decreased the relative abundances of plant–pathogenic fungi, for instance, Fusarium. In addition, the result of metabolomic analysis showed that intercropping promoted the synthesis of functional compounds, such as trehalose and ethanolamine, which enhanced plant disease resistance in bulk soils. Moreover, the co-occurrence networks of microbiomes and metabolomes of bulk soils revealed that Bacillus was significantly correlated with Fusarium, Alternaria, and trehalose under intercropping patterns. Furthermore, analysis of microbiomes and metabolomes in the rhizosphere soil of caper spurge and honeysuckle revealed that Penicillium and Rhizomicrobium were significantly increased by intercropping and showed more dynamic connections with other genera and metabolites compared with single planting.ConclusionsOverall, intercropping pecans with caper spurge and honeysuckle can improve soil conditions and promote plant growth through microbiological and metabolomics integrated analyses. This study provides valuable information and theoretical basis for optimizing land resource utilisation and improving soil conditions in tree fields like pecan fields via intercropping, thereby reducing production losses and ensuring economic benefits.Graphical

Effects of burning on vegetation, soil physicochemistry and prokaryotic microbial communities in surface and subsurface peat

Prescribed burning is a common management strategy in peatlands that has the potential to affect soil physicochemistry, alter biogeochemical cycles and trigger changes in vegetation structure. How burning affects prokaryotic community composition across different soil profiles is not well understood. This study explored the effects of prescribed burning on the diversity of prokaryotic communities in peat soils. Soil samples were collected from Moor House Nature Reserve, UK, a long-term monitoring site initiated in 1954 subject to three burning treatments: Burning at short rotations every 10 years, burning at long rotations every 20 years and a non-burn control. Observed species richness for archaea was highest in the topsoil of the non-burn control plots and highest for bacteria in the topsoil of the non-burn control and plots under a long rotation regime. Community composition was significantly different between different burn treatments and soil depth. Archaeal community structure was shaped by NH4+ and pH in the topsoil; by Pb, moisture and Al in the 20–40 cm profile; and by total N, total C, Al, Ca, Fe and pH in the 40–60 cm profile. Bacterial community structure was shaped by NH4+, heather cover, pH and Mg in the topsoil; by Fe, K and Pb in the 20–40 cm profile; and by Al, Ca and Fe in the 40–60 cm profile. A co-occurrence network analysis revealed that the topsoil of the non-burn control plots had a more complex network structure with more positive links than those under a rotational burn, but a higher average connectivity with a higher number of negative links was observed in the long rotation 20–40 cm profile. The results provide a new insight into the response processes of soil prokaryotic communities to burning in peatland soils, providing valuable knowledge that can support the evaluation and management of ecosystem services in peatlands.

Effects of soil compaction on above- and belowground interactions during the early stage of forest development

Forested green spaces in urban and peri-urban areas are expected to serve multiple roles, including providing ecosystem services and maintaining species diversity and soil health, both of which are particularly important for human health. However, soil compaction is a major cause of soil degradation in urban areas and brownfields (abandoned, previously developed land). We examined the effects of compaction on soil physicochemical properties, tree species richness, tree basal area, and the functional diversity of microbial communities in an immature volcanic soil through a long-term (14-year) field experiment. Our experimental results showed that soil compaction reduced not only both tree species richness and biomass but also the multifunctionality of soil microbial communities. Furthermore, tree species richness was significantly positively related to soil microbial decomposition activity. These findings provide evidence of above- and belowground interactions and underscore their importance in the design of urban forests using ecosystem-based solutions.

Soil metabolic processes influenced by rice roots co-regulates the environmental evolution of antibiotic resistome

Plant root activities lead to significant differences in metabolites between the rhizosphere and non-rhizosphere soil, profoundly affecting microbial distribution. However, how this process drives the migration and propagation of manure-derived antibiotic resistance genes (ARGs) in farmland ecosystems remains unclear. Herein, we used a rice pot microcosm experiment to explore the characteristics of antibiotic resistome and bacterial communities in rhizosphere and non-rhizosphere soils and the driving effects of rhizosphere metabolites on ARG propagation. The results showed significant differences in some ARGs and bacterial diversity in rhizosphere and non-rhizosphere soils with varied differential ARGs between different growth stages of rice (P < 0.05). The biosynthesis of secondary metabolites and glutathione metabolism were found to be the main pathways affecting ARG differences in rhizosphere and non-rhizosphere soils under manure application. Structural equation modeling (SEM) analysis further indicated that ARG distribution differences between rhizosphere and non-rhizosphere soils were mainly regulated by differential metabolites, which influenced the ARG distribution by altering the succession of soil microbial communities. These results demonstrate the role of differential metabolites resulting from rice root activities in co-regulating ARG distribution, providing new insights into the regulatory mechanisms of soil ARG dynamics in paddy fields.

Stochastic Processes Dominate the Assembly of Soil Bacterial Communities of Land Use Patterns in Lesser Khingan Mountains, Northeast China

To meet the demands of a growing population, natural wetlands are being converted to arable land, significantly impacting soil biodiversity. This study investigated the effects of land use changes on bacterial communities in wetland, arable land, and forest soils in the Lesser Khingan Mountains using Illumina MiSeq 16S rRNA sequencing. Soil physicochemical properties and enzyme activities were measured using standard methods, while microbial diversity was assessed through sequencing analysis. Our findings revealed that forest soils had significantly higher levels of total potassium (2.62 g·kg−1), electrical conductivity (8.22 mS·cm−1), urease (0.18 mg·g−1·d−1), and nitrate reductase (0.13 mg·g−1·d−1), attributed to rich organic matter and active microbial communities. Conversely, arable soils showed lower total potassium (1.94 g·kg−1), reduced electrical conductivity, and suppressed enzyme activities due to frequent tilling and fertilization. Wetland soils exhibited the lowest values primarily due to water saturation, which limits organic matter decomposition and microbial activity. Land use changes notably reduced microbial diversity, with conversion from forest to arable land leading to habitat loss. Forest soils supported higher abundances of Proteobacteria (37.59%) and Actinobacteriota (34.73%), while arable soils favored nitrogen-fixing bacteria. Wetlands were characterized by chemoheterotrophic and anaerobic bacteria. Overall, these findings underscore the profound influence of land use on soil microbial communities and their functional roles, highlighting the need for sustainable management practices.

Soil Biocrusts May Exert a Legacy Impact on the Rhizosphere Microbial Community of Plant Crops

Biological soil crusts (biocrusts) play important ecological roles in many ecosystems, but their legacy effects in subtropical agricultural systems are poorly understood. This study investigated how biocrusts impact soil properties and subsequent crop rhizosphere microbiomes. Soil with (+BC) and without (−BC) biocrusts was cultivated and used to grow pepper plants in a greenhouse experiment. Soil physicochemical properties and microbial communities in the pre-planting soils, and microbial communities in crop rhizosphere were analyzed. The results showed that soils with biocrust had significantly higher organic matter, total nitrogen, alkaline hydrolyzable nitrogen, total phosphorus, and total potassium content. Microbial community structures differed significantly among treatments, with −BC soils exhibiting higher microbial diversity in pre-planting conditions, while +BC soils showed higher diversity in crop rhizosphere soils. Soil properties, especially extractable potassium, total nitrogen, and organic matter content, were significantly correlated with rhizosphere microbial community structure. Additionally, our results showed that the first principal coordinate (PCoA1) of soil microbial community structure was significantly correlated with rhizosphere microbiota. Multiple regression analysis revealed that pre-planting soil microbial diversity indices and certain soil physicochemical properties could predict crop rhizosphere soil microbial diversity. Our results demonstrate that biocrusts can enhance soil fertility and alter microbial communities in subtropical agricultural soils, with persistent effects on the crop rhizosphere microbiome. This study provides new insights into the ecological legacy of biocrusts in managed subtropical ecosystems and their potential agricultural implications.

Synergistic effect of microplastics and cadmium on microbial community and functional taxa in wheat rhizosphere soil

Synergistic effect of microplastics and cadmium on microbial community and functional taxa in wheat rhizosphere soil

Effect of P Reduction on phoD-Harboring Bacteria Community in Solar Greenhouse Soil

Phosphorus (P) enrichment frequently occurs in the soil used in greenhouse vegetable production (GVP). Minimizing the application of P fertilizer represents a crucial approach to mitigating the accumulation of P in the soil and enhancing its utilization efficiency. However, the changes in bacterial communities and the turnover mechanism of soil P fractions related to soil P cycling after P fertilizer reduction are still unclear. To unravel these complexities, we devised three experimental treatments: conventional nitrogen (N), P, and potassium (K) fertilizer (N1P1K1); conventional N and K fertilizer without P (N1P0K1); and no fertilizer (N0P0K0). These experiments were conducted to elucidate the effects of P reduction on cucumber plant growth, soil P fractions, and the phoD-harboring bacterial community in the P-rich greenhouse soil. The results showed that there were no significant differences between the N1P1K1 and N1P0K1 treatments in terms of plant growth, yield, and P uptake, and the values for the N0P0K0 treatment were significantly lower than those for the N1P1K1 treatment. In a state of P depletion (N0P0K0, N1P0K1), the main P sources were Resin-Pi, NaHCO3-Pi, NaHCO3-Po, and NaOH-Pi. The contents of NaOH-Po and CHCl-Po in the N1P0K1 treatment increased significantly. Without P fertilizer, alkaline phosphatase (ALP) activity, phoD gene abundance, and bacterial community diversity were significantly increased. The abundance of Ensifer in the N0P0K0 and N1P0K1 treatments was 8 and 10.58 times that in the N1P1K1 treatment, respectively. Additionally, total phosphorus (TP) and available nitrogen (AN) were key factors affecting changes in the phoD bacterial community, while Shinella, Ensifer and Bradyrhizobium were the main factors driving the change in soil P fractions, and NaHCO3-Pi and NaOH-Pi were key factors affecting crop yield. Therefore, reducing the application of P fertilizer will increases the diversity of phoD-gene-harboring bacterial communities and promote organic P mineralization, thus maintaining the optimal crop yield.

Interplay between vanadium distribution and microbial community in soil-plant system

Soil-plant system play an essential role in distribution and transformation of vanadium (V). V shapes the diversity of soil communities, while soil microorganisms mediate V transformation. Plants also absorb V from surrounding soil. However, the study of microbial response to V stress in different soil-plant compartments is limited, and the metabolic functions driving V transformation across these systems remain elusive. The study investigates the distribution of V in soil-plant systems nearby a V smelter. 16S rRNA sequencing and metagenomics are utilized to reveal the microbial adaptation and V transformation in bulk soil, rhizosphere, and endosphere. Bothriochloa ischaemum (L.) Keng. (BK) exhibits higher phytoextraction potential (TF = 0.74 ± 0.26). Environmental variables, including pH, V, OM, and AP, show significant (p < 0.05) influence in soil community composition, with homogeneous selection governing the assembly processes in bulk soil and rhizosphere, while stochastic process dominates endospheric assembly. Metagenomic investigation revealed a coordinated metabolic pathway between functional taxa in soil and plants, which lead to root uptake and translocation. V stress is mitigated through Nocardioide, Microvirga, and Solirubrobacter, putatively harboring V(V) reduction genes n arG and mtrC in soil. In rhizosphere, citrate synthase gltA and alkaline phosphatase phoD exhibit functional potential to facilitate formation of V-complexation to increase V mobility. In endoshere, endophytic Enterobacter further detoxifies V(V), and likely promotes V translocation through siderophore biosynthesis gene, iucA. These findings enhance our understanding on interplay between V and microbial community in soil-plant systems, which is instrumental in developing mitigation plan for V contaminated sites.

Impacts of the coexistence of polystyrene microplastics and pesticide imidacloprid on soil nitrogen transformations and microbial communities

The pollution of agricultural soils by microplastics (MPs) and pesticides has attracted significant attention. However, the combined impact of MPs and pesticides on soil nitrogen transformation and microbial communities remains unclear. In this study, we conducted a 28-day soil incubation experiment, introducing polystyrene microplastics (PS-MPs) at concentrations of 0.1% and 10% (w/w) and pesticide imidacloprid at concentrations of 0.1 mg/kg and 1.0 mg/kg. Our aim was to investigate the individual and combined effects of these pollutants on nitrogen transformations and microbial communities in agricultural soils. Imidacloprid accelerated the decline in soil pH, while PS-MPs slowed the process. Imidacloprid hindered soil nitrification and denitrification processes, however, the presence of PS-MPs mitigated the inhibitory effects of imidacloprid. Based on microbial community and functional annotation analyses, this is mainly attributed to the different effects of PS-MPs and imidacloprid on soil microbial communities and the expression of key nitrogen transformation-related genes. Variance partitioning analysis and partial least squares path modeling analyses revealed that PS-MPs and imidacloprid indirectly influenced the microbial community structure, primarily through changes in soil pH. This study elucidates the mechanism through which the combined stress of MPs and pesticides in agricultural soils influence soil nitrogen transformation and microbial communities. The findings offer valuable insights for the systematic evaluation of the ecological risks posed by the coexistence of these pollutants.