Affect Soil Microbial Communities Research Articles

Polyethylene microplastics distinctly affect soil microbial community and carbon and nitrogen cycling during plant litter decomposition

Plant litter is an important input source of carbon and nitrogen in soil. While microplastics (MPs) and plant litter are ubiquitously present in soil, their combined impact on soil biogeochemical processes remains poorly understood. To address this gap, we examined the soil changes resulting from the coexistence of plant litter (Alfalfa) and polyethylene microplastics (PE). The soil changes included physicochemical properties, composition of soil dissolved organic matter, and structure of the soil microbial community. The results showed that the addition of polyethylene (PE) inhibited the degradation of humus-like substances and decreased the quantity of humic acid-like compounds in soil dissolved organic matter (DOM). PE negatively impacted plant litter decomposition, disrupted soil organic carbon (SOC) breakdown, interfered with the nitrogen cycle, and significantly altered microbial community structures during the process. By day 35, SOC and total nitrogen (TN) levels were reduced by 39.8% and 10.1%, respectively, in the presence of PE. Furthermore, PE significantly decreased the abundance of nitrogen-fixing microbes, including Streptomyces (43.1%) and Bacillus (45.9%), which play key roles in nitrate reduction to ammonium. This study highlights the environmental effects of MPs on plant litter decomposition and their potential implications for soil biogeochemical processes.

Soil properties and microbial evolution during cropping system conversion: Insights from a 105-year study in southern China

Understanding the mechanisms by which soil environments and microbial communities evolve in response to long-term changes in cropping systems is essential for the development of effective ecological conservation and restoration strategies. In this study, variations of soil characteristics and the succession of microbial community assemblages and functions were investigated in southern Chinese deciduous forests and adjacent converted tea plantations at different ages (20, 40, 60, and 105 years). The results revealed significant alterations in soil properties and the emergence of distinct diversity patterns and assembly mechanisms for bacterial and fungal communities over the century-long succession period. Bacterial α-diversity exhibited a declining trend throughout succession, while fungal α-diversity experienced a rebound in the later stages. Null model analysis indicated that stochastic processes primarily drove the assembly of the bacterial community in both forests and tea plantations, whereas fungal community assembly gradually shifted from stochastic dominance to deterministic dominance. The strength of interactions between bacterial taxa in tea plantations decreased over time, but the topological properties of fungal networks were restored in tea plantations aged 60 and 105 years. The functional groups of bacteria associated with carbon cycling and saprotrophic fungi significantly increased after tea cultivation, which was closely linked to the proliferation of r-strategists stimulated by sufficient nutrients in tea plantations. It is noteworthy that in addition to typical environmental variables such as nutrients and pH, soil polyphenols in tea plantations also have a profound effect on the composition and assembly processes of bacterial and fungal communities. These findings advance the current understanding of how long-term cropping system changes affect soil microbial community assembly and functionality, and highlight the distinct strategies by which bacteria and fungi respond to cropping system change.

Effects of irrigation-mediated continuously moist and dry-rewetting pattern on soil physicochemical properties, structure and bacterial community

The drying-rewetting cycles (DRW) shaped by climate change are known to affect the physicochemical cycles of natural soils. In irrigated soils, changes in irrigation methods make DRW cycles more repetitive and frequent. However, how irrigation regimes affect the physicochemical properties of irrigated soils and their selection of microbial communities have yet to be discovered. Two irrigation methods for two DRW patterns were selected: (1) continuous irrigation for constantly moist (including three soil wetness, low for CL, medium for CM, and high for CH) and (2) intermittent irrigation for DRW (including three intermittent irrigation frequencies, low for DL, medium for DM and high for DH), to determine the selection of soil physicochemical properties and microbial communities and their effect on yield by mediating soil DRW patterns with different irrigation methods. The results revealed that the DRW pattern mediated by irrigation regimes significantly affected soil physicochemical properties. Constantly moist treatments maintained a more stable soil hydrothermal status, with less soil salinity and slight alkalinity than DRW treatments. The water-stable aggregate was greater in CM, but it was progressively enhanced with increased intermittent frequency. In addition, SOM and TN in CM were 15 %, 25 %, and 35 % higher than in DL, DM, and DH, respectively. High-throughput sequencing results showed that CM had the largest Chao1 index (2610.10), Shannons index (10.23), and Simpsons index (0.9982). The results of the Mental tests indicated that soil moisture patterns exhibited a high degree of explanation by environmental factors. The RDA analysis demonstrated that the PC1 axis (28.7 %) significantly separated the soil bacterial communities of different treatments. These results extend the theoretical understanding of how continuously moist soil and continuous irrigation affect soil physicochemical properties and microbial community diversity. This study provides theoretical guidance for strengthening the application and popularization of continuous irrigation in irrigated soil in the future.

Trade-offs and adaptation to metalliferous soils: The role of soil microbiome in metal tolerance and uptake in Arabidopsis halleri ecotypes from a reciprocal transplant experiment

Soil contamination with trace metal elements is a worldwide issue, prompting research on plant species capable of hyperaccumulating metals to reduce soil toxicity. Previous research suggests that both plant species and their populations can affect soil microbial communities, yet little is known about how different populations of hyperaccumulator species influence these microbial communities to enhance metal-uptake and tolerance. This study evaluated the effect of soil origin, soil microbiome, and plant population on phytoextraction efficiencies of Cd and Zn among four A. halleri populations: two each from metalliferous and non-metalliferous sites. In a controlled transplant experiment, clonal replicates of A. halleri were grown in native and three non-native soils for six months. Biogeochemical analyses of plants and soils were conducted, alongside sequencing of root-associated soil bacterial/archaeal and fungal DNA. Soil treatments primarily differed in pH, total Cd, Pb, and Zn, as well as acid and alkaline phosphatase enzyme activities. A combined effect of soil origin and population was noted for arylsulfatase and β-glucosidase activities, as well as ammonium and nitrate concentrations. Both non-metallicolous and metallicolous populations accumulated high levels of Cd and Zn in metalliferous soils with the non-metallicolous population NM_PL14 outperforming the metallicolous populations in Zn hyperaccumulation. Interestingly, non-metallicolous populations grown in metalliferous soils exhibited no trade-offs in plant performance despite higher Cd and Zn accumulation. Soil origin had a stronger effect on the bacterial/archaeal and fungal community composition than plant ecotype. Partial least square regression models explained 66 % and 79 % of the variability in A. halleri Cd and Zn hyperaccumulation. There was a positive association between Zn-uptake and specific microbial taxa (e.g., Cornebacteriales, Microbacteriaceae, Propionibacteriales, Rhizobiaceae, Basidiomycota, Oidiodendron, Phallaceae) and functional activity (e.g., arylsulfatase, S oxidation) in metalliferous soils. Taken together, our findings suggest that non-metallicolous A. halleri populations may be better suited for Zn phytoextraction applications.

Karst Ecosystem: Moso Bamboo Intercropping Enhances Soil Fertility and Microbial Diversity in the Rhizosphere of Giant Lily (Cardiocrinum giganteum)

Intercropping affects soil microbial community structure significantly; however, the effects on understory medicinal plants in karst areas remain unclear. We investigated the effects of four intercropping systems (Moso bamboo, Chinese fir, bamboo-fir mixed forest, and forest gap) on the rhizosphere microbial communities of giant lily (Cardiocrinum giganteum), an economically important medicinal plant in China. We assessed the intercropping impact on rhizosphere microbial diversity, composition, and co-occurrence networks and identified key soil properties driving the changes. Bacterial and fungal diversity were assessed by 16S rRNA and ITS gene sequencing, respectively; soil physicochemical properties and enzyme activities were measured. Moso bamboo system had the highest fungal diversity, with relatively high bacterial diversity. It promoted a distinct microbial community structure with significant Actinobacteria and saprotrophic fungi enrichment. Soil organic carbon, total nitrogen, and available potassium were the most influential drivers of microbial community structure. Co-occurrence network analysis revealed that the microbial network in the Moso bamboo system was the most complex and highly interconnected, with a higher proportion of positive interactions and a greater number of keystone taxa. Thus, integrating Moso bamboo into intercropping systems can enhance soil fertility, microbial diversity, and ecological interactions in the giant lily rhizosphere in karst forests.

Enhanced bioremediation of bensulfuron-methyl contaminated soil by Hansschlegelia zhihuaiae S113: Metabolic pathways and bacterial community structure

Bensulfuron-methyl (BSM), a widely used herbicide, can persist in soil and damag sensitive crops. Microbial degradation, supplemented with exogenous additives, provides an effective strategy to enhance BSM breakdown. Hansschlegelia zhihuaiae S113 has been shown to efficiently degrade this sulfonylurea herbicide. However, depending solely on a single strain for degradation proves inefficient and unlikely to achieve ideal remediation in practical applications. This study assessed the impact of various carbon sources on the degradation efficiency of S113 in BSM-polluted soil. Among these, glucose was the most effective, achieving a 98.7 % degradation rate after 9 d of inoculation. In addition, seven intermediates were detected during BSM degradation in soil through the cleavage of the phenyl ring ester bond, the pyrimidine rings, and urea bridge peptide bond, among other pathways. 2-amino-4,6-dimethoxy pyrimidine (ADMP), and 2-(aminosulfonylmethyl)-methyl benzoate(MSMB) were the primary intermediates. These metabolites were less toxic to maize, sorghum, and bacteria than the BSM. Community structure analysis indicated that variations in exogenous carbon sources and environmental pollutants significantly improved the ecological functions of soil microbial communities, enhancing pollutant degradation. Addition of carbon sources notably affected soil microbial community structure, modifying metabolic activities and interaction patterns. Specifically, glucose substantially increased the richness and diversity of soil bacterial communities. These findings offer valuable insights for field remediation practices and contributed to the development of more robust soil pollution management strategies.

Adaptation strategies of soil microorganisms in resource changes and stoichiometric imbalances induced by secondary succession on the loess plateau

Sequestering farmland for secondary succession is an effective method of restoring ecosystem services to degraded farmland, but long-term secondary succession often alters ecosystem environments, resources, and substrate stoichiometry. Currently, it is not known how resource changes and stoichiometric imbalances due to secondary succession affect soil microbial community structure and function, hindering our understanding of the natural resilience for degraded ecosystems. Here, we assessed nutrient limitation elements, community structure, metabolic functions, co-occurrence network complexity, and community stability of soil microorganisms during secondary succession of abandoned farmlands on the Loess Plateau. Results showed that secondary succession significantly altered plant characteristics and soil properties, as well as causing stoichiometry imbalances in nutrient resources. Along the secondary succession chronosequence, microbial nutrient metabolism shifted from phosphorus (P) limitation to carbon (C) and nitrogen (N) co-limitation. Microbial diversity, eutrophic flora, plant growth-promoting bacteria, and metabolism functional groups increased significantly during the 20 years after the abandonment of the farmlands, but decreased significantly with long-term succession. However, oligotrophic flora and P-solubilizing bacteria became dominant after 30 years of secondary succession on abandoned farmlands. The topological features of microbial co-occurring networks, including nodes, degree, closeness, betweenness, and eigenvector complexity, natural connectivity, and community stability first increased and then decreased with secondary succession. Correlation and random forest analyses indicated that secondary succession-induced stoichiometry imbalances in C:N and N:P, as well as changes in soil organic C and lignin phenols, were the key factors influencing microbial community structure and function. Overall, these results enhance our understanding of the adaptation strategies of soil microbial communities in ecologically managed regions to changes in ecosystem resources and stoichiometric imbalances.

Effects of tree species identity on soil microbial communities in Juglans nigra and Quercus rubra plantations.

Understanding how different tree species affect soil microbial communities is crucial for sustainable forestry and ecosystem management practices. Despite Black walnut (Juglans nigra L.) forestry having a rich history, the overall comprehension of how this hardwood species influences soil remains incomplete. In earlier studies, we examined the effects of hardwood plantations on soil chemical properties and their interaction with microbial biomass, however, we highlight the importance of studying the soil microbial communities and their relationship with soil properties in greater depth. Building on this foundation, our research focused on evaluating microbiome compositions beneath J. nigra and another hardwood, Northern red oak (Quercus rubra L.) after a decade of establishment. We uncovered intriguing patterns within the soil bacterial/archaeal and fungal structures by conducting meticulous analyses utilizing amplicon sequencing alongside soil chemical properties. Our findings underscore that tree species play a pivotal role in shaping soil microbial structures, a role that surpasses even seasonal and depth influences. Most notably, J. nigra stands out for its ability to enhance microbial diversity, as evidenced by increased alpha-diversity indices compared to baseline values. Conversely, Q. rubra tends to decrease these indices. Significant disparities in microbial composition between the two tree species were evident, with J. nigra exhibiting enrichment in certain taxa such as Nitrospira, Geobacter, and Bacillus while Q. rubra showed enrichment in others like Acidobacteriota and ectomycorrhizal fungi. Furthermore, we also observed differences in co-occurrence networks by delving deeper into the interconnections within the soil microbiota. In both fungal and bacterial/archaeal communities, J. nigra and Q. rubra notably decreased the number of connections within their networks, while Q. rubra increased some, suggesting a more interconnected network. These differences were further highlighted by network metrics with Q. rubra displaying a higher mean degree and clustering coefficient. Additionally, our analysis revealed that tree species influence soil chemical properties, either directly or indirectly, thereby affecting soil bacterial and fungal communities. In conclusion, our study elucidates the intricate interplay between tree species and soil microbiota, emphasizing the need to consider these relationships in forestry and ecosystem management practices.

Invasive plants and their root traits are linked to the homogenization of soil microbial communities across the United States

Although the impacts of invasive plants on soil ecosystems are widespread, the role and impacts of invader root traits in structuring microbial communities remain poorly understood. Here, we present a macroecological study investigating how plant invaders and their root traits affect soil microbial communities, spanning data from 377 unique plots across the United States sampled multiple times, totaling 632 sampling events and 94 invasive plant species. We found that native and invasive plants harbor different root traits on average, with invasive plants possessing higher specific root lengths and native plants having higher root tissue density. We also show that soil microbial communities experiencing heavy plant invasions were more similar to each other in composition across ecosystem types and geographical regions than plots with higher proportions of native plants, which displayed highly variable microbial communities across the continent. Root traits of invasive plants in highly invaded plots explained two times more variation in microbial composition than native plants. This work represents an important step toward understanding macroscale and cross-scale patterns of the relationship between plant invasions, root traits, and soil microbial composition. Our findings provide insights into how invasive plants may impact ecosystem functioning at the macroscale via their homogenizing influence on microbial communities.

Prescribed burning alters soil microbial community structure by changing soil physicochemical properties in temperate forests of northern China

Prescribed burning is commonly used to maintain forest ecosystem functions and reduce the risk of future wildfires. Although many studies have investigated the response of microbial community to wildfires in forest ecosystems, the effects of prescribed burnings on soil microbial community structure are less studied. It is also unclear that how post-fire soil physiochemical properties changes affected soil microbial communities. Here, we studied the impacts of prescribed burning on soil microbiome in three typical temperate forests of northern China by collecting soil physicochemical and high-throughput sequencing for 16S rRNA and 18S rRNA was applied to analyze the diversity and community composition of soil microbes (bacteria and fungi). Compared with pre-fire condition, prescribed burning significantly decreased Chao1 index and altered soil bacterial communities (P < 0.05), whereas it had no significant effect on fungal diversity and community structure of the (P > 0.05). Planctomycetes and Actinobacteria made the greatest contributions to the bacterial community dissimilarity between the pre-fire and post-fire conditions. The main variables influencing the post-fire soil microbial community structure are soil pH, available phosphorus, total nitrogen, and the ratio of soil total carbon to soil total nitrogen, which could account for 73.5% of the variation in the microbial community structure in these stands. Our findings demonstrated a great discrepancy in the responses of bacteria and fungi to prescribed burning. Prescribed burning altered the soil microbial structure by modifying the physicochemical properties. Our results pointed that it is essential to evaluate the impact of prescribed burnings on forest ecosystem functions. These findings provide an important baseline for assessing post-fire microbial recovery in the region and offer critical guidance for restoration efforts.

Global perspective of ecological risk of plastic pollution on soil microbial communities.

The impacts of plastic pollution on soil ecosystems have emerged as a significant global environmental concern. The progress in understanding how plastic pollution affects soil microbial communities and ecological functions is essential for addressing this issue effectively. A bibliometric analysis was conducted on the literature from the Web of Science Core Collection database to offer valuable insights into the dynamics and trends in this field. To date, the effects of plastic residues on soil enzymatic activities, microbial biomass, respiration rate, community diversity and functions have been examined, whereas the effects of plastic pollution on soil microbes are still controversial. To include a comprehensive examination of the combined effects of plastic residue properties (Type, element composition, size and age), soil properties (soil texture, pH) at environmentally relevant concentrations with various exposure durations under field conditions in future studies is crucial for a holistic understanding of the impact of plastic pollution on soil ecosystems. Risk assessment of plastic pollution, particularly for nanoplasctics, from the perspective of soil food web and ecosystem multifunctioning is also needed. By addressing critical knowledge gaps, scholars can play a pivotal role in developing strategies to mitigate the ecological risks posed by plastic pollution on soil microorganisms.

How do high phosphate concentrations affect soil microbial communities after a century of ecosystem self-reclamation?

The use of rock phosphate (RP) instead of soluble phosphate fertilizers is preferred for the development of more sustainable agriculture. However, the impact of high concentrations in RP on bacterial and fungal communities remains poorly documented. Thus, next-generation sequencing was used to characterize bacterial and fungal communities in the soils and roots of four plant species growing naturally in a self-restored ecosystem, on former open-pit phosphate mines where past exploitation generated locally a substantial phosphate enrichment of the soil. Our results show that bacterial communities are dominated by Actinobacteria and Proteobacteria phyla, while the Ascomycota and Basidiomycota phyla predominate in the fungal community. The alpha and beta diversities of both bacterial and fungal communities differ significantly between the root and soil compartments but are not significantly affected by RP inputs. However, Amplicon Sequence Variants (ASVs) indicative of RP-enriched soils have been identified; among them are bacteria representative of Streptomyces, Bacillus, Mycobacterium or Agromyces. Implications of these results open new ways of reflection to understand the microbial response following RP-inputs and long-term soil restoration, as well as to formulate microbial-based bioinoculants for sustainable agriculture applications based on microorganisms better adapted to high concentrations of RP.

Control of inorganic and organic phosphorus molecules on microbial activity, and the stoichiometry of nutrient cycling in soils in an arid, agricultural ecosystem

Background The dynamics of carbon (C), nitrogen (N), and phosphorus (P) in soils determine their fertility and crop growth in agroecosystems. These dynamics depend on microbial metabolism, which in turn depends on nutrient availability. Farmers typically apply either mineral or organic fertilizers to increase the availability of nutrients in soils. Phosphorus, which usually limits plant growth, is one of the most applied nutrients. Our knowledge is limited regarding how different forms of P impact the ability of microbes in soils to produce the enzymes required to release nutrients, such as C, N and P from different substrates. Methods In this study, we used the arable layer of a calcareous soil obtained from an alfalfa cropland in Cuatro Cienegas, México, to perform an incubation experiment, where five different phosphate molecules were added as treatments substrates: three organic molecules (RNA, adenine monophosphate (AMP) and phytate) and two inorganic molecules (calcium phosphate and ammonium phosphate). Controls did not receive added phosphorus. We measured nutrient dynamics and soil microbial activity after 19 days of incubation. Results Different P molecules affected potential microbial C mineralization (CO2-C) and enzyme activities, specifically in the organic treatments. P remained immobilized in the microbial biomass (Pmic) regardless of the source of P, suggesting that soil microorganisms were limited by phosphorus. Higher mineralization rates in soil amended with organic P compounds depleted dissolved organic carbon and increased nitrification. The C:N:P stoichiometry of the microbial biomass implied a change in the microbial community which affected the carbon use efficiency (CUE), threshold elemental ratio (TER), and homeostasis. Conclusion Different organic and inorganic sources of P affect soil microbial community structure and metabolism. This modifies the dynamics of soil C, N and P. These results highlight the importance of considering the composition of organic matter and phosphate compounds used in agriculture since their impact on the microbial activity of the soil can also affect plant productivity.

Impact mechanisms of various surfactants on the biodegradation of phenanthrene in soil: Bioavailability and microbial community responses

The present study was conducted to systematically explore the mechanisms underlying the impact of various surfactants (CTAB, SDBS, Tween 80 and rhamnolipid) at different doses (10, 100 and 1000 mg/kg) on the biodegradation of a model polycyclic aromatic hydrocarbon (PAH) by indigenous soil microorganisms, focusing on bioavailability and community responses. The cationic surfactant CTAB inhibited the biodegradation of phenanthrene within the whole tested dosage range by decreasing its bioavailability and adversely affecting soil microbial communities. Appropriate doses of SDBS (1000 mg/kg), Tween 80 (100, 1000 mg/kg) and rhamnolipid at all amendment levels promoted the transformation of phenanthrene from the very slow desorption fraction (Fvslow) to bioavailable fractions (rapid and slow desorption fractions, Frapid and Fslow), assessed via Tenax extraction. However, only Tween 80 and rhamnolipid at these doses significantly improved both the rates and extents of phenanthrene biodegradation by 22.1–204.3 and 38.4–76.7 %, respectively, while 1000 mg/kg SDBS had little effect on phenanthrene removal. This was because the inhibitory effects of anionic surfactant SDBS, especially at high doses, on the abundance, diversity and activity of soil microbial communities surpassed the bioavailability enhancement in dominating biodegradation. In contrast, the nonionic surfactant Tween 80 and biosurfactant rhamnolipid enhanced the bioavailability of phenanthrene for degradation and also that to specific degrading bacterial genera, which stimulated their growth and increased the abundance of the related nidA degradation gene. Moreover, they promoted the total microbial/bacterial biomass, community diversity and polyphenol oxidase activity by providing available substrates and nutrients. These findings contribute to the design of suitable surfactant types and dosages for mitigating the environmental risk of PAHs and simultaneously benefiting microbial ecology in soil through bioremediation.

Bacterial and fungal communities exhibit contrasting patterns in response to marsh erosion: A fine-scale observation

Coastal salt marshes, especially their seaward boundaries, are experiencing severe erosion and area loss worldwide because of human disturbances and natural changes. However, how marsh erosion affects soil microbial communities and their potential functions remains poorly understood in subtropical coastal ecosystems. Herein, simultaneous measurements of the abundance, diversity, and composition of bacterial and fungal communities were conducted along a marsh erosion gradient, based on Illumina sequencing of 16S rRNA and ITS genes. Our results indicate that marsh erosion is often accompanied by a loss of plant biomass and a decrease in soil total carbon, total nitrogen, and organic matter concentrations, but an increase in soil water content. We found that the abundance of bacteria and fungi tended to decrease with erosion, especially for bacterial communities. Marsh erosion had opposite effects on the alpha-diversity of bacterial and fungal communities, with bacterial diversity decreasing but fungal diversity increasing with marsh erosion. The beta-diversity and composition of bacterial and fungal communities were altered by marsh erosion, and in particular bacterial communities were clustered into three groups: uneroded, eroding, and eroded. Network analysis demonstrated that the inter-relationships of the bacterial community did not significantly change with the erosion gradient, but the complexity of the fungal networks increased. The diversity and composition of the bacterial and fungal communities can be jointly explained by plant biomass, soil nutrient dynamics, and bulk density. We conclude that marsh erosion-induced changes in soil properties and plant loss altered the diversity and composition of bacterial and fungal communities, which decrease bacterial abundance and diversity but increase fungal diversity and network complexity, suggesting that these microbial taxa contribute differently to soil function and nutrient cycling as marsh erosion continues.

Insights in to iron-based nanoparticles (hematite and magnetite) improving the maize growth (Zea mays L.) and iron nutrition with low environmental impacts

The possible potential application of Fe-NPs on Fe nutrition, heavy metals uptake and soil microbial community needs to be investigated. In the current research, a pot experiment was used to examine the implications of Fe-NPs (α-Fe2O3 and Fe3O4) on maize growth, Fe uptake and transportation, soil microbial community, and environmental risk. Fe3O4, α-Fe2O3, FeSO4 at a rate of 800 mg Fe kg−1 were applied in soils with four replications under a completely randomized design for a period of 60 days. Results showed that Fe uptake by maize roots were increased by 107–132% than control, with obvious variations across different treatments (Fe3O4> α-Fe2O3> FeSO4> control). Similarly, plant height, leaf surface area, and biomass were increased by 40–64%, 52–91% and 38–109% respectively, with lower values by FeSO4 application. The elevated level of chlorophyll contents and carotenoids and significant effects with control on antioxidant enzymes activities (i.e., catalase, and superoxide dismutase) suggested that application of Fe-NPs improved overall biochemical processes. The differential expression of important Fe transporters (i.e., ZmYS1 and ZmFER1) as compared to control indicated the plant strategic response for efficient uptake and distribution of Fe. Importantly, Fe-NPs reduced the heavy metals uptake (i.e., chromium, cadmium, arsenic, nickel, copper) by complex formation, and showed no toxicity to the soil microbial community. In summary, the application of Fe-NPs can be a promising approach for improving crop productivity and Fe nutrition without negatively affecting soil microbial community, and fostering sustainable agricultural production.

Soil fungal community structure and function response to rhizoma perennial peanut cultivars

BackgroundCrop-associated microorganisms play a crucial role in soil nutrient cycling, and crop growth, and health. Fine-scale patterns in soil microbial community diversity and composition are commonly regulated by plant species or genotype. Despite extensive reports in different crop or its cultivar effects on the microbial community, it is uncertain how rhizoma peanut (RP, Arachis glabrata Benth.), a perennial warm-season legume forage that is well-adapted in the southern USA, affects soil microbial community across different cultivars.ResultsThis study explored the influence of seven different RP cultivars on the taxonomic composition, diversity, and functional groups of soil fungal communities through a field trial in Marianna, Florida, Southern USA, using next-generation sequencing technique. Our results showed that the taxonomic diversity and composition of the fungal community differed significantly across RP cultivars. Alpha diversity (Shannon, Simpson, and Pielou’s evenness) was significantly higher in Ecoturf but lower in UF_Peace and Florigraze compared to other cultivars (p < 0.001). Phylogenetic diversity (Faith’s PD) was lowest in Latitude compared to other cultivars (p < 0.0001). The dominant phyla were Ascomycota (13.34%), Mortierellomycota (3.82%), and Basidiomycota (2.99%), which were significantly greater in Florigraze, UF_Peace, and Ecoturf, respectively. The relative abundance of Neocosmospora was markedly high (21.45%) in UF_Tito and showed large variations across cultivars. The relative abundance of the dominant genera was significantly greater in Arbrook than in other cultivars. There were also significant differences in the co-occurrence network, showing different keystone taxa and more positive correlations than the negative correlations across cultivars. FUNGuild analysis showed that the relative abundance of functional guilds including pathogenic, saprotrophic, endophytic, mycorrhizal and parasitic fungi significantly differed among cultivars. Ecoturf had the greatest relative abundance of mycorrhizal fungal group (5.10 ± 0.44), whereas UF_Peace had the greatest relative abundance of endophytic (4.52 ± 0.56) and parasitic fungi (1.67 ± 0.30) compared to other cultivars.ConclusionsOur findings provide evidence of crop cultivar’s effect in shaping fine-scale fungal community patterns in legume-based forage systems.Graphical abstract

Stand development reduces soil carbon mineralization in rubber plantations through regulating microbial metabolic strategy and substrate availability

Forest age, a critical variable for land-use decision makers, is known to change soil microbial communities. However, how such changes affect microbial metabolic strategy and the associated soil C mineralization processes in different forest ages remains unknown, especially in tropical region. To address this issue, three different aged rubber plantations, namely 4-year-old (Young, YRP), 15-year-old (Mature, MRP), and 31-year-old (Old, ORP), were studied to reveal the soil mineralization characteristics. Furthermore, to understand the mechanism from the coupled perspective of decomposers and substrate availability, the microbial metabolic strategy was deciphered by 2D-COS-Biolog assay, and linked with soil microbial composition and labile-/recalcitrant- organic pools. Results showed that YRP was characterized by having more copiotrophic taxa (e.g., actinobacteria) and the largest G(-)/G(+) ratio and invertase activity. Thus, YRP exhibited a preferential utilization for carbohydrate and the largest SOC mineralization rate. In contrast, regardless of abundant labile C and N pools in MRP, the soil microbial communities were shifted to oligotrophic taxa in utilizing resistant polymer, and MRP contained abundant G(+), fungi and arbuscular mycorrhizal fungi related to aggregate formation. As a result, the soil mineralization rate in MRP was reduced by 66 % compared with YRP. However, the SOC mineralization rate was unchanged from MRP to ORP, primarily because the increased proportion of recalcitrant nutrient pool, and soil microorganism had greater priority in utilizing relatively resistant amine. The structural equation modeling revealed that the variations in mineralization were mainly regulated by soil microbial composition and metabolic strategy, and partially affected by soil C and N pools. Furthermore, random forest model indicated that soil pH, NH4-N and C/N were also the crucial factor for mineralization by affecting soil microbial communities during stand development. In summary, these findings improve our understanding in soil C budget and contribute to the C accurate management during plantation development.

Safe production of rice in Cd-polluted paddy fields by rhizosphere application of zero-valent iron nanoplates at specific growth stages

Nanoscale zero-valent iron (nZVI) is efficient in immobilizing soil heavy metals for rice safe production, but is still limited in field application due to the relatively short effective duration and the required high dose. Herein, ball-milled ZVI nanoplates (10, 100, and 1000 mg kg−1) of ∼5 μm in width and ∼100 nm in thickness were injected into rice rhizosphere at different growth stages in three paddy fields with different Cd pollution levels (0.76–27.34 mg kg−1) to explore the optimum application time and dose for rice safe production. Although applying ZVI nanoplates at the pre-sowing, jointing, and flowering stages all promoted root iron plaque (IP) formation and Cd sequestration by IP, it could not prevent Cd accumulation in brown rice due to the later IP weathering and subsequent Cd remobilization. In contrast, the brown rice Cd content was significantly reduced to the safe level by the 100 and 1000 mg kg−1 ZVI nanoplate treatments at the grain-filling stage when the grain Cd accumulation occurs; moreover, the 100 mg kg−1 ZVI nanoplate treatment at this stage significantly increased the rice yield and thousand kernel weight, without adversely affecting soil microbial community. The findings provide a feasible nZVI application technique for safe production of rice in Cd-polluted paddy fields.

Untargeted metabolomics to study changes in soil microbial community in response to tillage practices

Soil microbes are the main drivers of nutrient turnover in agro-ecosystems. The series of biochemical processes involved by these microorganisms are inseparable from the regulation of metabolites in the root-zone soils. Therefore, understanding the evolution of microbial communities driven by root-zone soil metabolites will help optimize agricultural management practices. Based on a field experiment, we explore the changes in soil properties, microbes, and metabolites under three tillage practices such as no-tillage with straw mulching (NTS), rotary tillage, and plough tillage with straw returning (RTS and PTS) based on untargeted metabolomics. We found that NTS helped to enhance nutrient contents and enzyme activities in the 0–20 cm soil layer. Specifically, compared with RTS and PTS, NTS increased grain yield by 6.4 % and 8.5 %, and SOC by 13.3 % and 5.7 %, respectively, but decreased pH by 2.8 % and 1.1 %. In addition, compared with NTS, RTS and PTS decreased the fungal richness by 16.5 % and 8.1 %, and decreased the fungal shannon index by 16.4 % and 9.2 %. However, tillage practices did not result in substantial differences in the alpha diversity of bacterial community. Both bacterial and fungal community composition were substantially affected by tillage practices and they were both significantly correlated with soil metabolites. In the symbiotic networks, NTS significantly increased the abundance of microorganisms with high connectivity, while RTS significantly increased the concentration of metabolites with high connectivity. Amino acids, as the main drivers, were significantly and positively associated with bacterial and fungal community composition, mainly enriched in the metabolic pathways of D − glutamine and D − glutamate metabolism and arginine and proline metabolism, and correlated with soil properties negatively and carbohydrates positively, directly or indirectly affecting soil microbial community composition. Our findings would provide new insight into metabolomics for the in-depth understanding of the metabolic mechanism for soil microbial community changes in dryland wheat fields under different tillage practices.